BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716351.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 = 817,674 number of mapped reads = 736,352 (90.05%) number of supplementary alignments = 14,343 (1.75%) number of secondary alignments = 0 number of mapped bases = 57,412,310 bp number of sequenced bases = 57,386,352 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,154 duplication rate = 1.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2839 >>>>>>> ACTG content number of A's = 14,679,258 bp (25.58%) number of C's = 11,366,363 bp (19.81%) number of T's = 18,108,511 bp (31.56%) number of G's = 13,228,160 bp (23.05%) number of N's = 4,060 bp (0.01%) GC percentage = 42.86% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 405,354 number of insertions = 4,827 mapped reads with insertion percentage = 0.65% number of deletions = 13,778 mapped reads with deletion percentage = 1.84% homopolymer indels = 43.05% >>>>>>> Coverage mean coverageData = 0.0185X std coverageData = 0.1848X There is a 1.74% of reference with a coverageData >= 1X There is a 0.08% 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 4547801 0.018245896366292303 0.28235019931959304 chr2 243199373 4732850 0.01946078208022354 0.2122349815939131 chr3 198022430 3756126 0.018968184563738562 0.1426938127304155 chr4 191154276 3667086 0.01918390776672974 0.16572436192950615 chr5 180915260 3433366 0.018977757874045563 0.14374290220418653 chr6 171115067 3329330 0.01945667356107221 0.1521425060365419 chr7 159138663 3376929 0.021220041291914085 0.24694084151183568 chr8 146364022 2894931 0.01977897956370726 0.20312996423551424 chr9 141213431 2428348 0.01719629629280801 0.17053599243671783 chr10 135534747 2774136 0.020468079672587576 0.1927714883214228 chr11 135006516 2921862 0.021642377616795917 0.19727181128211377 chr12 133851895 2613156 0.0195227419081366 0.145239036082103 chr13 115169878 1832508 0.01591134793074974 0.13073934735131604 chr14 107349540 1647101 0.015343344740927628 0.1341648142130626 chr15 102531392 1622560 0.015825007037844566 0.13083541202843285 chr16 90354753 1648317 0.01824272598033664 0.1438572058660109 chr17 81195210 1536538 0.018923998102843752 0.15273523706252598 chr18 78077248 1476790 0.018914473010114292 0.2387287240600331 chr19 59128983 1095780 0.01853202853159169 0.23222346090223753 chr20 63025520 1226639 0.019462576429357503 0.14932748699454212 chr21 48129895 759567 0.0157816051749126 0.142835214879866 chr22 51304566 660771 0.012879379975653629 0.11770808000876823 chrMT 16571 21865 1.3194737794942972 1.3064806124392465 chrX 155270560 3238853 0.02085941468878582 0.16339664103548146 chrY 59373566 169100 0.002848068785358117 0.09910297877393993