pibase | pibase step 1 | pibase_bamref example: 1000 Genomes NA12878 SOLiD chr22
The tab-separated text file (above, and in full detail below) shows example output from pibase_bamref. The header lines all start with '#' so that they can be grep'd away from the linux command line or easily parsed with scripts.
Columns 1 and 2 are the genomic coordinates of interest (chromosome number, and 1-based position in chromosome.
Columns 3, 4, and 5 are as extracted from the reference sequence: reference base, window of 13 bases, GC-content in this window. Column 6 denotes whether homopolymeric runs or STRs occur.
Column 7 reports how many reads in the BAM file at the genomic coordinate of interest were ignored due to indels-in-a-read or data conflicts in the BAM-file.
The remaining columns are counts of reads which support each nucleotide (A, C, G, T, or N, on each strand), for 10 different criteria: There are 5 filter levels. Within each filter level there are unique-start-point counts and coverage counts. The most stringent filter level is the leftmost group and the least stringent level is the rightmost group:
The rightmost group is unfiltered. (The coverage counts correspond to those in a genome viewer).
The next group applies a PHRED-like base quality filter (user-specifiable, default=20) so that sequencing errors are eliminated.
The next group additionally applies a mapped-read-length filter (user-specifiable, default=49) to filter shortened reads which were mapped by the aligner, because genomic lower complexity loci may lead to alignment of read fragments from other genomic loci.
The next group additionally applies a maximal mismatch filter (user-specifiable, default=1) to filter reads with multiple mismatches, because on average in the human genome there is only about 1 mismatch in 1000 nucleotides.
The leftmost group additionally applies a minimal mapping quality filter (user-specifiable, default=20) so that multiple-mappable reads or otherwise poorly mapped reads are eliminated.
# Position Info (1-based coordinates) generated by pibase_bamref v1.4 from file NA12878.chrom22.SOLID.bfast.CEU.high_coverage.20100125.bam # Reference: hg19.1000G.quick.fasta # Positions of interest taken from file: hg19_chr22_genomic_coords_of_interest.txt # Max fragment length considered: 50 bases # Base quality value threshold QVmin= 20 # Mapped-length-of-read threshold MLmin= 34 bases # Mismatch-in-read threshold MMmax= 1 # Read-mapping quality value threshold RQVmin= 20 # Column "Ign" denotes number of ignored reads due to indels (usually bad mapping!) # Column "RefSeqcontext" denotes the poi-Refbase and the +-6 Refbases # Column "Class" denotes context class (e.g. stretches or STRs) # Date: 2011_10_28__15:19:27 # MapQV>RQVmin and MM<=MMmax and Read>MLmin and BaseQVs>=QVmin MM<=MMmax and Read>MLmin and BaseQVs>=QVmin Read>MLmin and BaseQVs>=QVmin BaseQVs>=QVmin No QV-Filtering # Unique start points (on +- strands) Coverage Unique start points (on +- strands) Coverage Unique start points (on +- strands) Coverage Unique start points (on +- strands) Coverage Unique start points (on +- strands) Coverage # C Pos[1] Ref RefSeqContext GC[%] Class Ign A+ A- C+ C- G+ G- T+ T- N+ N- A+ A- C+ C- G+ G- T+ T- N+ N- A+ A- C+ C- G+ G- T+ T- N+ N- A+ A- C+ C- G+ G- T+ T- N+ N- A+ A- C+ C- G+ G- T+ T- N+ N- A+ A- C+ C- G+ G- T+ T- N+ N- A+ A- C+ C- G+ G- T+ T- N+ N- A+ A- C+ C- G+ G- T+ T- N+ N- A+ A- C+ C- G+ G- T+ T- N+ N- A+ A- C+ C- G+ G- T+ T- N+ N- 22 17662444 C TTTTCT[C]ACTCTC 38 5 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 3 1 0 0 0 0 0 0 0 0 3 1 0 0 0 0 0 0 0 0 5 2 0 0 0 0 0 0 0 0 5 2 0 0 0 0 0 0 22 17662793 A GAAATC[A]TAGGAC 38 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 22 17669306 T TAGTCA[T]GCAAGG 46 1 1 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 1 3 0 0 0 0 0 0 0 0 1 3 0 0 0 0 0 0 0 0 2 4 0 0 0 0 0 0 0 0 2 4 0 0 0 0 0 0 0 0 2 5 0 0 0 0 0 0 0 0 2 5 0 0 22 19958811 C CCTGAC[C]GCGGGC 84 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 22 19958829 G GGGCCC[G]GGGGGA 92 9 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 22 19968971 G GGGCCT[G]GGCCAA 76 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 22 19969075 A ACCCCC[A]CTGCTG 69 8 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 0 22 19969106 A GTGGCC[A]CTGGGC 76 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 22 19969495 G GGATGT[G]ACAATA 38 1 3 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 2 4 0 0 0 0 0 0 0 0 3 5 0 0 0 0 0 0 0 0 4 4 0 0 0 0 0 0 0 0 6 5 0 0 0 0 22 22318538 C CCGTGT[C]GGCCCA 76 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 22318671 G CATGGC[G]TGCTGC 69 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 22 23503121 G GCAGTC[G]GTGCTG 69 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 0 0 1 0 0 1 1 0 0 0 0 22 23503170 A GTCGGC[A]ATGGAG 61 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 22 24579503 T GACTCC[T]CCGGGC 76 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 3 0 0 0 0 0 0 0 0 1 3 0 0 22 24582041 A CATTCA[A]TGGGCG 53 1 1 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 6 4 0 0 0 0 0 0 0 0 6 4 0 0 0 0 0 0 0 0 7 4 0 0 0 0 0 0 0 0 7 4 0 0 0 0 0 0 0 0 22 30823196 T GGTGAC[T]GTGGCT 61 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 22 30823250 G CATTCC[G]GGCTTC 61 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 22 30856121 G CGAAGC[G]TAGGAC 61 1 4 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 3 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 2 4 0 0 0 0 0 0 0 0 2 5 0 0 0 0 22 30857373 A TAGAAC[A]TCTGTC 38 1 3 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 2 1 1 1 0 0 0 0 0 0 2 1 1 1 0 0 0 0 0 0 22 30857448 A CGCACC[A]TCAGAT 53 1 2 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 0 0 0 3 3 0 0 0 0 0 0 0 0 3 3 0 0 0 0 0 0 0 0 3 4 0 0 0 0 0 0 0 0 22 30860830 C TTCCTG[C]GAGTGT 53 1 2 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 2 4 0 0 0 0 0 0 22 30864610 A GGCCCA[A]TGATGT 53 1 3 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 3 0 0 0 0 0 0 0 0 1 3 0 0 0 0 0 0 0 0 1 3 0 0 0 0 0 0 0 0 1 3 0 0 0 0 0 0 0 0 22 30864627 G CCACAC[G]GGGCAG 76 4 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 3 3 0 0 0 0 0 0 0 0 4 3 0 0 0 0 22 30951948 G GGTGCT[G]CTGGCC 76 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 4 3 0 0 0 0 0 0 0 0 4 4 0 0 0 0 22 30953280 C GGGGCA[C]GGCATA 69 4 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 22 30953295 C AGTACA[C]CAGCAG 53 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 22 31487701 C ACTCAG[C]ACCAGT 53 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 22 31491295 G ATGGAA[G]CAGAGC 53 1 10 0 0 1 0 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 2 0 0 1 0 0 0 0 0 0 2 0 0 1 0 0 0 0 0 0 2 0 1 1 0 0 0 0 0 0 2 0 1 1 0 0 0 0 0 0 2 0 4 1 0 0 0 0 0 0 2 0 4 1 0 0 0 0 22 31491332 C TGGAAG[C]GGCCAA 61 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 22 31655196 G ACTGGT[G]CAGCAT 53 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 0 0 0 0 0 0 0 0 1 3 0 0 0 0 22 31658205 C CCCGTC[C]GCACAC 76 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 2 4 0 0 0 0 0 0 22 31663842 C GAACCT[C]CTGACA 53 1 4 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 1 3 0 0 0 0 0 0 0 0 1 3 0 0 0 0 0 0 0 3 2 3 0 0 0 0 0 0 0 3 2 3 0 0 0 0 22 33670584 G GTAGGC[G]TTGGGC 69 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 4 0 0 0 0 22 33673125 C CAGTCA[C]GTCTCA 53 1 2 0 0 2 2 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 3 2 0 0 0 0 0 0 0 0 2 3 0 0 1 0 0 0 0 0 3 3 0 0 1 0 0 0 22 34000460 G CACAGC[G]GGCACC 76 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 1 0 0 0 0 0 0 0 0 7 1 0 0 0 0 22 34000484 C GAAGAG[C]GTGGCC 69 1 6 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 5 2 0 0 0 0 0 0 0 0 5 2 0 0 0 0 0 0 22 34022284 G GTATCC[G]GCGCAG 69 1 2 0 3 0 0 0 1 0 0 0 0 0 3 0 0 0 1 0 0 0 0 0 3 0 0 0 1 0 0 0 0 0 3 0 0 0 1 0 0 0 0 1 3 0 0 0 1 0 0 0 0 1 3 0 0 0 1 0 0 0 0 1 4 0 0 0 1 0 0 0 0 1 4 0 0 0 1 0 0 0 0 1 4 0 0 2 1 0 0 0 0 1 4 0 0 2 1 0 0 0 0 22 39095987 A CACACA[A]CTCATG 46 500 2 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 3 5 0 0 0 0 0 0 0 0 3 5 0 0 0 0 0 0 0 0 22 39440149 C AGTGCG[C]CCCACC 76 3 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 0 0 0 1 0 0 0 0 1 2 0 0 0 1 0 0 22 39627630 G CACCTG[G]ACAGGT 61 1 3 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 1 2 0 0 0 0 22 40283427 A TCATCT[A]TGTGCT 38 1 1 2 1 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 2 3 0 0 1 0 0 0 0 0 2 3 0 0 1 0 0 0 0 0 2 4 0 0 1 0 0 0 0 0 2 4 0 0 1 0 0 0 0 0 22 40417495 C CAAGTA[C]GCCTTG 53 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 22 40417571 G GCGGGC[G]GCAACC 84 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 22 40417780 C CCGAAA[C]GGCATG 61 1 1 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 22 40417820 A CCCGCC[A]GGCGCT 84 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 22 40417943 G CCCAAC[G]AGAATT 46 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 2 5 0 0 0 0 0 0 0 0 3 5 0 0 0 0 22 45312244 G GGCGGC[G]GCATTG 76 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 22 45312345 C GGCTGC[C]GGGCGC 92 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 22 50616806 A TGGGCT[A]GGCCTG 69 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 22 21998280 G CTGTGC[G]CTTCCA 61 1 4 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 1 1 0 0 1 1 0 0 0 0 1 1 0 0 1 1 0 0 0 0 1 1 0 0 3 1 0 0 0 0 1 1 0 0 3 1 0 0 0 0 22 22318354 T GCGTCA[T]GGCCTT 61 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 1 0 0 0 2 2 0 0 0 0 1 0 0 0 2 2 0 0 0 0 1 0 0 0 2 2 0 0 0 0 1 0 0 0 2 2 0 0 22 24580807 C CAACTC[C]GGCTCT 61 1 2 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 4 1 0 0 0 0 0 0 0 0 5 1 0 0 0 0 0 0 22 24580897 C AAATTA[C]GCAGGG 46 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 3 4 0 0 0 0 0 0 0 0 3 4 0 0 0 0 0 0 22 45279003 G GGGTGT[G]TGGCTG 69 1000 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
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