BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081040.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,115,910 number of mapped reads = 1,710,492 (80.84%) number of supplementary alignments = 8,045 (0.38%) number of secondary alignments = 0 number of mapped bases = 108,680,482 bp number of sequenced bases = 108,642,136 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,226 duplication rate = 1.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2498 >>>>>>> ACTG content number of A's = 31,646,295 bp (29.13%) number of C's = 20,809,208 bp (19.15%) number of T's = 32,159,379 bp (29.6%) number of G's = 24,025,874 bp (22.11%) number of N's = 1,380 bp (0%) GC percentage = 41.27% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 877,425 number of insertions = 7,102 mapped reads with insertion percentage = 0.41% number of deletions = 22,252 mapped reads with deletion percentage = 1.29% homopolymer indels = 46.29% >>>>>>> Coverage mean coverageData = 0.0351X std coverageData = 0.2756X There is a 3.14% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% 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 8713546 0.034958974084160856 0.4161036254812238 chr2 243199373 9401538 0.03865773946711614 0.2922715567786562 chr3 198022430 7302972 0.036879519153461555 0.20800881120708417 chr4 191154276 7300852 0.03819350606627288 0.22087840696162056 chr5 180915260 6785256 0.037505161256159374 0.21088795802635746 chr6 171115067 6482491 0.037883811832887866 0.26476528136637956 chr7 159138663 6015042 0.03779748985323573 0.4161558187902063 chr8 146364022 5184032 0.03541875885318319 0.28962306677901417 chr9 141213431 4469300 0.03164925579918811 0.2548470065864257 chr10 135534747 5027414 0.03709317434296019 0.25341073953325455 chr11 135006516 4922430 0.036460684608733994 0.26676317320824966 chr12 133851895 4933556 0.03685832016050277 0.20987093573503146 chr13 115169878 3496507 0.030359561551328552 0.18869911327900737 chr14 107349540 3380978 0.031495039475716434 0.20226007000446466 chr15 102531392 3258288 0.03177844303528036 0.20337665950025263 chr16 90354753 3013254 0.03334914766465025 0.21481574760754493 chr17 81195210 2772201 0.03414242047037011 0.22324846475301216 chr18 78077248 2818035 0.0360929089099042 0.47583512066472605 chr19 59128983 2048132 0.03463837691914978 0.3099572873154354 chr20 63025520 2256700 0.03580613059598715 0.20891664273022575 chr21 48129895 1443210 0.02998572924374757 0.1976335649399719 chr22 51304566 1211089 0.02360587164892887 0.16612374239654834 chrMT 16571 31172 1.8811176151107356 1.8539200443027126 chrX 155270560 6163016 0.03969210905145187 0.24019531391723087 chrY 59373566 249471 0.004201718320236989 0.09573137728637787