BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708584.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 5,814,182 number of mapped reads = 5,561,275 (95.65%) number of supplementary alignments = 163 (0%) number of secondary alignments = 0 number of mapped bases = 277,400,594 bp number of sequenced bases = 277,376,922 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,100 duplication rate = 1.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7784 >>>>>>> ACTG content number of A's = 85,774,777 bp (30.92%) number of C's = 52,793,308 bp (19.03%) number of T's = 85,277,305 bp (30.74%) number of G's = 53,521,936 bp (19.3%) number of N's = 9,596 bp (0%) GC percentage = 38.33% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 401,820 number of insertions = 17,347 mapped reads with insertion percentage = 0.31% number of deletions = 14,015 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.49% >>>>>>> Coverage mean coverageData = 0.0896X std coverageData = 0.3138X There is a 8.2% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 21444231 0.08603481473372136 0.309670480479643 chr2 243199373 23966271 0.09854577626727681 0.3277906265028231 chr3 198022430 20950028 0.10579623732523634 0.33899342234431074 chr4 191154276 20862000 0.10913697792457439 0.34363930679116883 chr5 180915260 19039968 0.10524246545039927 0.33778376602085475 chr6 171115067 17486235 0.10218991995602585 0.33221711758045785 chr7 159138663 14660498 0.09212404907536517 0.3169998623153649 chr8 146364022 14647252 0.10007412887300951 0.32940780968271927 chr9 141213431 10974583 0.07771628323371026 0.2929742267231325 chr10 135534747 11756577 0.08674216214090104 0.30670353838658304 chr11 135006516 13702036 0.10149166429863282 0.3358410742670461 chr12 133851895 12666703 0.09463222765729241 0.3218958598008311 chr13 115169878 12033483 0.10448463790158742 0.3404364999360191 chr14 107349540 9889498 0.09212426993166435 0.32048310782655964 chr15 102531392 7407533 0.07224648817798163 0.282831604055217 chr16 90354753 5247308 0.05807450992644515 0.25155744884969694 chr17 81195210 4577305 0.056374076746645525 0.24826552637986304 chr18 78077248 7850296 0.10054524462747458 0.3305012461389435 chr19 59128983 2429067 0.041080818183529384 0.2106750822187249 chr20 63025520 4155965 0.06594098707951954 0.2684321691743407 chr21 48129895 3520037 0.07313618697900753 0.28658733513999174 chr22 51304566 1602402 0.03123312650184001 0.18394430238587192 chrMT 16571 350 0.021121235894031743 0.15702863087371075 chrX 155270560 16174632 0.10417062964157532 0.3373581303091158 chrY 59373566 356336 0.006001593369008693 0.08145959685269415