BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173979.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 = 3,521,090 number of mapped reads = 3,444,889 (97.84%) number of supplementary alignments = 422,998 (12.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,724,015 number of mapped paired reads (second in pair) = 1,720,874 number of mapped paired reads (both in pair) = 3,397,622 number of mapped paired reads (singletons) = 47,267 number of mapped bases = 386,651,482 bp number of sequenced bases = 386,381,221 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,752,506 duplication rate = 64.94% >>>>>>> Insert size mean insert size = 938,824.617 std insert size = 9,176,476.3731 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 52.6456 >>>>>>> ACTG content number of A's = 115,926,540 bp (30%) number of C's = 76,349,761 bp (19.76%) number of T's = 114,944,820 bp (29.75%) number of G's = 79,157,088 bp (20.49%) number of N's = 3,012 bp (0%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 3,248,180 number of insertions = 44,168 mapped reads with insertion percentage = 1.23% number of deletions = 110,098 mapped reads with deletion percentage = 3.12% homopolymer indels = 41.45% >>>>>>> Coverage mean coverageData = 0.1249X std coverageData = 2.3095X There is a 2.66% of reference with a coverageData >= 1X There is a 1.99% of reference with a coverageData >= 2X There is a 1.48% of reference with a coverageData >= 3X There is a 1.2% of reference with a coverageData >= 4X There is a 0.9% of reference with a coverageData >= 5X There is a 0.75% of reference with a coverageData >= 6X There is a 0.56% of reference with a coverageData >= 7X There is a 0.49% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.25% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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% 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 27824398 0.11163221133960585 1.340273489562064 chr2 243199373 36540035 0.15024724179695972 7.033628024820623 chr3 198022430 28033278 0.1415661751045071 1.1474489975950448 chr4 191154276 24862707 0.1300661827727045 1.4255341202173317 chr5 180915260 24026884 0.13280739280920803 1.10668307227172 chr6 171115067 24017279 0.1403574765277683 1.2202550080378913 chr7 159138663 24582186 0.15447023078232094 1.5461913634230748 chr8 146364022 20477468 0.13990779783299478 1.6126373935941467 chr9 141213431 17242857 0.12210493632153163 1.2500211683416447 chr10 135534747 18204956 0.1343194745477335 1.6533763402132053 chr11 135006516 16383827 0.12135582404037447 1.0803650906567936 chr12 133851895 17937117 0.1340071950419529 1.1362857411882694 chr13 115169878 12406061 0.10771966781105734 0.9902451745376728 chr14 107349540 11418264 0.10636528111811192 0.994932004606289 chr15 102531392 10671585 0.10408114814241476 0.9785087055100292 chr16 90354753 12561198 0.13902088803230972 1.3246950252062921 chr17 81195210 10283155 0.12664731084506092 1.1240034452836252 chr18 78077248 10908867 0.1397188973668744 1.4634478599334617 chr19 59128983 7288691 0.1232676536986946 1.2279146771206364 chr20 63025520 7891047 0.1252039967302134 1.1382124879884807 chr21 48129895 5608271 0.11652364917895625 1.305119365225138 chr22 51304566 4591518 0.08949530924791373 1.0140513357844976 chrMT 16571 418591 25.260455011767547 23.18958564502513 chrX 155270560 9452338 0.06087656282040845 0.7453736286958653 chrY 59373566 3018904 0.05084592695678747 1.049414109610568