BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618611.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 = 46,595,358 number of mapped reads = 45,156,555 (96.91%) number of supplementary alignments = 150,241 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 22,786,283 number of mapped paired reads (second in pair) = 22,370,272 number of mapped paired reads (both in pair) = 44,437,424 number of mapped paired reads (singletons) = 719,131 number of mapped bases = 4,239,965,862 bp number of sequenced bases = 4,236,990,051 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,486,870 duplication rate = 27.99% >>>>>>> Insert size mean insert size = 65,216.8843 std insert size = 2,543,385.6617 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 51.7706 >>>>>>> ACTG content number of A's = 1,162,873,021 bp (27.45%) number of C's = 908,624,211 bp (21.45%) number of T's = 1,180,549,232 bp (27.86%) number of G's = 984,792,838 bp (23.24%) number of N's = 150,749 bp (0%) GC percentage = 44.69% >>>>>>> Mismatches and indels general error rate = 0.0123 number of mismatches = 51,107,748 number of insertions = 774,083 mapped reads with insertion percentage = 1.68% number of deletions = 2,159,755 mapped reads with deletion percentage = 4.66% homopolymer indels = 52.68% >>>>>>> Coverage mean coverageData = 1.3696X std coverageData = 5.8112X There is a 22.99% of reference with a coverageData >= 1X There is a 16.58% of reference with a coverageData >= 2X There is a 12.67% of reference with a coverageData >= 3X There is a 10.26% of reference with a coverageData >= 4X There is a 8.43% of reference with a coverageData >= 5X There is a 7.1% of reference with a coverageData >= 6X There is a 6.02% of reference with a coverageData >= 7X There is a 5.19% of reference with a coverageData >= 8X There is a 4.5% of reference with a coverageData >= 9X There is a 3.93% of reference with a coverageData >= 10X There is a 3.45% of reference with a coverageData >= 11X There is a 3.05% of reference with a coverageData >= 12X There is a 2.71% of reference with a coverageData >= 13X There is a 2.42% of reference with a coverageData >= 14X There is a 2.17% of reference with a coverageData >= 15X There is a 1.95% of reference with a coverageData >= 16X There is a 1.75% of reference with a coverageData >= 17X There is a 1.59% of reference with a coverageData >= 18X There is a 1.44% of reference with a coverageData >= 19X There is a 1.31% of reference with a coverageData >= 20X There is a 1.19% of reference with a coverageData >= 21X There is a 1.09% of reference with a coverageData >= 22X There is a 0.99% of reference with a coverageData >= 23X There is a 0.91% of reference with a coverageData >= 24X There is a 0.84% of reference with a coverageData >= 25X There is a 0.77% of reference with a coverageData >= 26X There is a 0.71% of reference with a coverageData >= 27X There is a 0.65% of reference with a coverageData >= 28X There is a 0.6% of reference with a coverageData >= 29X There is a 0.56% of reference with a coverageData >= 30X There is a 0.51% of reference with a coverageData >= 31X There is a 0.48% of reference with a coverageData >= 32X There is a 0.44% of reference with a coverageData >= 33X There is a 0.41% of reference with a coverageData >= 34X There is a 0.38% of reference with a coverageData >= 35X There is a 0.36% of reference with a coverageData >= 36X There is a 0.33% of reference with a coverageData >= 37X There is a 0.31% of reference with a coverageData >= 38X There is a 0.29% of reference with a coverageData >= 39X There is a 0.27% of reference with a coverageData >= 40X There is a 0.25% of reference with a coverageData >= 41X There is a 0.24% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 383993731 1.5405928757946805 6.288536500068953 chr2 243199373 372033738 1.5297479323682301 7.662359469254961 chr3 198022430 280925774 1.418656331002503 4.65832799211188 chr4 191154276 231854768 1.2129196000826055 4.963069819869586 chr5 180915260 253175621 1.3994155108861464 4.7398515251847675 chr6 171115067 240169201 1.403553791087257 4.836118964048354 chr7 159138663 216839434 1.362581725347284 4.786682646796721 chr8 146364022 213620986 1.4595184190825257 4.804099361372279 chr9 141213431 196151465 1.3890425550243872 5.798936912937507 chr10 135534747 221530624 1.6344932122830464 5.36495394981906 chr11 135006516 227508620 1.6851676996094025 6.040841645550274 chr12 133851895 201406315 1.5046952827974531 5.3235334443248785 chr13 115169878 122286510 1.0617924766751945 3.9997697440163456 chr14 107349540 140528063 1.3090700062617875 4.785550664568792 chr15 102531392 146537665 1.4291980450241035 5.111715442771025 chr16 90354753 155035949 1.7158582570636876 13.107383764552324 chr17 81195210 142834660 1.7591513095415359 6.001762842848076 chr18 78077248 114111089 1.4615152547384866 5.547719289382554 chr19 59128983 78072880 1.3203825947758987 5.528418338259849 chr20 63025520 124292784 1.9721024753147613 6.154351735202748 chr21 48129895 52680733 1.09455325011617 7.180797101559614 chr22 51304566 77937873 1.5191215729219891 6.055874339937341 chrMT 16571 63499 3.831935308671776 4.813703478389818 chrX 155270560 6792631 0.04374706319085859 1.1876608327643576 chrY 59373566 39581249 0.666647662698919 5.685866069092945