BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717081.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,000,695 number of mapped reads = 910,627 (91%) number of supplementary alignments = 2,726 (0.27%) number of secondary alignments = 0 number of mapped bases = 51,804,686 bp number of sequenced bases = 51,789,248 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,078 duplication rate = 2.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6728 >>>>>>> ACTG content number of A's = 12,058,190 bp (23.28%) number of C's = 10,261,451 bp (19.81%) number of T's = 17,059,425 bp (32.94%) number of G's = 12,409,688 bp (23.96%) number of N's = 494 bp (0%) GC percentage = 43.78% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 248,880 number of insertions = 2,935 mapped reads with insertion percentage = 0.32% number of deletions = 9,693 mapped reads with deletion percentage = 1.06% homopolymer indels = 44.84% >>>>>>> Coverage mean coverageData = 0.0167X std coverageData = 0.1706X There is a 1.53% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 6072032 0.024361150939720227 0.2370776198753114 chr2 243199373 5239018 0.021542070340781677 0.24629455091913138 chr3 198022430 3269119 0.016508831853038062 0.13851216714317116 chr4 191154276 2219762 0.011612410909395509 0.1170000484393941 chr5 180915260 3752913 0.020744037844016034 0.15468831867806068 chr6 171115067 1939291 0.011333256819517828 0.12507920643426965 chr7 159138663 3502837 0.02201122551846499 0.24908326729389582 chr8 146364022 2278853 0.015569762082651706 0.14537516960553504 chr9 141213431 1429116 0.010120255487595936 0.1312740254407229 chr10 135534747 2315426 0.01708363391123606 0.1805181130764568 chr11 135006516 2185703 0.01618961117402659 0.16194497179331468 chr12 133851895 2084681 0.015574534824478951 0.13424371833887835 chr13 115169878 1532165 0.013303521950418321 0.12379816093457674 chr14 107349540 1136695 0.010588727254909523 0.11193651642797098 chr15 102531392 2214317 0.02159647847168602 0.15921370004728355 chr16 90354753 1587789 0.017572833163519357 0.15100607773872962 chr17 81195210 1909266 0.023514515203544643 0.1703243239814369 chr18 78077248 1666302 0.02134171019962179 0.23685007761745777 chr19 59128983 841616 0.014233561230031642 0.1763021048416358 chr20 63025520 1329479 0.021094296405646473 0.15611152922164848 chr21 48129895 634272 0.013178337496892524 0.12316172470773078 chr22 51304566 600252 0.01169977736484507 0.11584481261854718 chrMT 16571 250 0.01508659706716553 0.12189746369838267 chrX 155270560 1957006 0.012603844540780944 0.13089746881456157 chrY 59373566 106526 0.0017941654371913588 0.05129084955479405