BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089610.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 16,682,719 number of mapped reads = 13,798,085 (82.71%) number of supplementary alignments = 597 (0%) number of secondary alignments = 0 number of mapped bases = 651,338,541 bp number of sequenced bases = 651,218,695 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,232,847 duplication rate = 15.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7084 >>>>>>> ACTG content number of A's = 188,497,691 bp (28.95%) number of C's = 137,144,809 bp (21.06%) number of T's = 186,301,957 bp (28.61%) number of G's = 139,263,196 bp (21.39%) number of N's = 11,042 bp (0%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 2,922,213 number of insertions = 25,886 mapped reads with insertion percentage = 0.19% number of deletions = 80,344 mapped reads with deletion percentage = 0.58% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 0.2104X std coverageData = 1.4167X There is a 8.31% of reference with a coverageData >= 1X There is a 4.09% of reference with a coverageData >= 2X There is a 2.46% of reference with a coverageData >= 3X There is a 1.62% of reference with a coverageData >= 4X There is a 1.11% of reference with a coverageData >= 5X There is a 0.78% of reference with a coverageData >= 6X There is a 0.56% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 51015655 0.20467614000448167 2.042367523836812 chr2 243199373 54000329 0.2220413989307448 1.7365878800427759 chr3 198022430 45304083 0.22878258286195155 1.0948123656994706 chr4 191154276 41852275 0.21894501067818123 1.142017449453375 chr5 180915260 39361163 0.21756684870032522 1.064566451251669 chr6 171115067 36564951 0.2136863318996918 1.2230515848964985 chr7 159138663 37567069 0.2360650032607098 1.9825273169413546 chr8 146364022 32962594 0.22520967618667925 1.6461883483753486 chr9 141213431 26901005 0.19049891224581889 1.2382508219413182 chr10 135534747 30623734 0.22594747603727036 1.4654108286015426 chr11 135006516 28377130 0.21019081775282608 1.309420907668163 chr12 133851895 28618004 0.21380350274458199 1.0943674378589516 chr13 115169878 20930679 0.18173744179880089 0.9851290856738113 chr14 107349540 20396412 0.18999999441078183 1.1609913431289722 chr15 102531392 18810198 0.1834579403740076 0.9923064411566379 chr16 90354753 18950778 0.20973747778381951 1.1300973361440119 chr17 81195210 18305814 0.22545435869923855 1.2457027687189333 chr18 78077248 17387107 0.22269108409148847 1.8255833069843972 chr19 59128983 13799940 0.2333870684026478 1.982262520177214 chr20 63025520 14384871 0.22823883087358898 1.173681230389563 chr21 48129895 8930911 0.1855584974785422 1.1259575140729006 chr22 51304566 7508373 0.14634902086492652 0.8875870535342911 chrMT 16571 76491 4.615955585058234 5.46493824022332 chrX 155270560 36742633 0.2366361852497988 1.2959325377242241 chrY 59373566 1966342 0.033118138802712305 0.6715589593378793