BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173945.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,330,950 number of mapped reads = 4,234,768 (97.78%) number of supplementary alignments = 512,022 (11.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,118,345 number of mapped paired reads (second in pair) = 2,116,423 number of mapped paired reads (both in pair) = 4,173,562 number of mapped paired reads (singletons) = 61,206 number of mapped bases = 481,953,882 bp number of sequenced bases = 481,662,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,441,044 duplication rate = 66.18% >>>>>>> Insert size mean insert size = 1,073,893.1615 std insert size = 9,723,228.4912 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 52.6554 >>>>>>> ACTG content number of A's = 143,604,083 bp (29.81%) number of C's = 95,930,056 bp (19.92%) number of T's = 142,258,796 bp (29.53%) number of G's = 99,865,529 bp (20.73%) number of N's = 3,618 bp (0%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 4,037,727 number of insertions = 52,407 mapped reads with insertion percentage = 1.19% number of deletions = 124,290 mapped reads with deletion percentage = 2.86% homopolymer indels = 41.43% >>>>>>> Coverage mean coverageData = 0.1557X std coverageData = 3.0288X There is a 3.14% of reference with a coverageData >= 1X There is a 2.42% of reference with a coverageData >= 2X There is a 1.85% of reference with a coverageData >= 3X There is a 1.51% of reference with a coverageData >= 4X There is a 1.15% of reference with a coverageData >= 5X There is a 0.95% of reference with a coverageData >= 6X There is a 0.72% of reference with a coverageData >= 7X There is a 0.62% of reference with a coverageData >= 8X There is a 0.47% of reference with a coverageData >= 9X There is a 0.42% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% 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 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 37206204 0.14927226199368226 1.4234886225478836 chr2 243199373 41131780 0.1691278209010843 9.652703720560364 chr3 198022430 33462969 0.16898575075560884 1.2909878723786496 chr4 191154276 31833578 0.16653343396827805 1.525293656013246 chr5 180915260 31011887 0.1714166455610212 1.29845990371969 chr6 171115067 26475243 0.1547218691151259 1.3204721798468777 chr7 159138663 25090829 0.1576664559510595 1.4592228347123135 chr8 146364022 25633390 0.17513450129158106 1.8338962874974567 chr9 141213431 21533626 0.15248992852528312 1.523515274840151 chr10 135534747 23664502 0.17460099733686743 1.8341387574114307 chr11 135006516 21948698 0.1625751011899307 1.2845766709791835 chr12 133851895 23602012 0.1763293078517865 1.3519941408772016 chr13 115169878 16162087 0.1403325876580333 1.1742207901750719 chr14 107349540 15334191 0.14284356504927734 1.190838144483444 chr15 102531392 14455280 0.14098394372720502 1.1737351023317817 chr16 90354753 15346677 0.16984913898220716 1.4627645976610206 chr17 81195210 13344100 0.16434590168557972 1.3366137200536392 chr18 78077248 14524054 0.18602159235940283 1.862147589557486 chr19 59128983 9389225 0.15879226267091387 1.3767696416676167 chr20 63025520 10580513 0.16787664742789904 1.2954009152621475 chr21 48129895 6802044 0.14132679907155418 1.4382722205368659 chr22 51304566 6182887 0.12051338666425908 1.3351141196086347 chrMT 16571 1087654 65.63599058596343 55.106439598387404 chrX 155270560 12329242 0.07940489169357025 0.867043316622685 chrY 59373566 3821210 0.06435877541867706 1.032076016021951