BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618643.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 51,261,122 number of mapped reads = 45,740,408 (89.23%) number of supplementary alignments = 208,548 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,637,073 number of mapped paired reads (second in pair) = 21,103,335 number of mapped paired reads (both in pair) = 41,668,568 number of mapped paired reads (singletons) = 4,071,840 number of mapped bases = 4,229,860,666 bp number of sequenced bases = 4,226,918,294 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,755,362 duplication rate = 18.17% >>>>>>> Insert size mean insert size = 141,683.0912 std insert size = 3,761,273.1812 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 53.2642 >>>>>>> ACTG content number of A's = 1,133,440,360 bp (26.81%) number of C's = 933,580,562 bp (22.09%) number of T's = 1,164,975,563 bp (27.56%) number of G's = 994,678,216 bp (23.53%) number of N's = 243,593 bp (0.01%) GC percentage = 45.62% >>>>>>> Mismatches and indels general error rate = 0.0148 number of mismatches = 61,492,823 number of insertions = 777,101 mapped reads with insertion percentage = 1.67% number of deletions = 2,132,867 mapped reads with deletion percentage = 4.55% homopolymer indels = 52.48% >>>>>>> Coverage mean coverageData = 1.3664X std coverageData = 5.4586X There is a 28.6% of reference with a coverageData >= 1X There is a 18.83% of reference with a coverageData >= 2X There is a 13.67% of reference with a coverageData >= 3X There is a 10.49% of reference with a coverageData >= 4X There is a 8.32% of reference with a coverageData >= 5X There is a 6.76% of reference with a coverageData >= 6X There is a 5.59% of reference with a coverageData >= 7X There is a 4.69% of reference with a coverageData >= 8X There is a 3.99% of reference with a coverageData >= 9X There is a 3.42% of reference with a coverageData >= 10X There is a 2.96% of reference with a coverageData >= 11X There is a 2.57% of reference with a coverageData >= 12X There is a 2.26% of reference with a coverageData >= 13X There is a 1.99% of reference with a coverageData >= 14X There is a 1.76% of reference with a coverageData >= 15X There is a 1.57% of reference with a coverageData >= 16X There is a 1.4% of reference with a coverageData >= 17X There is a 1.25% of reference with a coverageData >= 18X There is a 1.13% of reference with a coverageData >= 19X There is a 1.02% of reference with a coverageData >= 20X There is a 0.92% of reference with a coverageData >= 21X There is a 0.84% of reference with a coverageData >= 22X There is a 0.76% of reference with a coverageData >= 23X There is a 0.7% of reference with a coverageData >= 24X There is a 0.64% of reference with a coverageData >= 25X There is a 0.58% of reference with a coverageData >= 26X There is a 0.53% of reference with a coverageData >= 27X There is a 0.49% of reference with a coverageData >= 28X There is a 0.45% of reference with a coverageData >= 29X There is a 0.42% of reference with a coverageData >= 30X There is a 0.39% of reference with a coverageData >= 31X There is a 0.36% of reference with a coverageData >= 32X There is a 0.33% of reference with a coverageData >= 33X There is a 0.31% of reference with a coverageData >= 34X There is a 0.29% of reference with a coverageData >= 35X There is a 0.27% of reference with a coverageData >= 36X There is a 0.25% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 375875371 1.508021803484293 6.418276507674074 chr2 243199373 352491143 1.449391660232611 6.851478550121496 chr3 198022430 272202773 1.3746057605696487 4.621109158512633 chr4 191154276 215752536 1.128682760933896 4.284990899277379 chr5 180915260 237882630 1.3148842723383312 4.541271396673013 chr6 171115067 226513388 1.323748936731562 4.609125008881295 chr7 159138663 213197469 1.339696243394982 4.689882997224858 chr8 146364022 205939230 1.4070345101612471 4.95769007383455 chr9 141213431 183233127 1.2975616108357284 5.473307089832293 chr10 135534747 211148384 1.55789115834628 5.433901015298715 chr11 135006516 211904840 1.5695897226175364 5.970143741914676 chr12 133851895 189583268 1.4163659617968054 5.271744037363641 chr13 115169878 113396952 0.9846059922022319 3.926578364885695 chr14 107349540 132966151 1.238628046286924 4.68548141089407 chr15 102531392 136100370 1.3274019531501142 5.2192772262757705 chr16 90354753 147317859 1.630438400954956 9.366597338214058 chr17 81195210 138809666 1.7095794936671758 5.831896341476105 chr18 78077248 104454123 1.3378304906443423 5.084422969659977 chr19 59128983 90822660 1.53600916829569 5.895466539503153 chr20 63025520 116677665 1.8512765146562853 6.07345434528582 chr21 48129895 56611086 1.1762146167158687 6.707077113417733 chr22 51304566 75412871 1.4699056415368565 5.603663639515996 chrMT 16571 7102 0.4285800494840384 1.3203735171030975 chrX 155270560 214666046 1.3825289610599718 4.362556800780244 chrY 59373566 6893956 0.1161115369085293 3.355359940444676