BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173839.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 = 3,691,330 number of mapped reads = 3,595,546 (97.41%) number of supplementary alignments = 355,776 (9.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,803,538 number of mapped paired reads (second in pair) = 1,792,008 number of mapped paired reads (both in pair) = 3,531,482 number of mapped paired reads (singletons) = 64,064 number of mapped bases = 421,842,055 bp number of sequenced bases = 421,606,615 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,777,351 duplication rate = 63.97% >>>>>>> Insert size mean insert size = 902,221.4728 std insert size = 8,652,102.9331 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.717 >>>>>>> ACTG content number of A's = 127,615,142 bp (30.27%) number of C's = 81,792,728 bp (19.4%) number of T's = 127,285,696 bp (30.19%) number of G's = 84,908,190 bp (20.14%) number of N's = 4,859 bp (0%) GC percentage = 39.54% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 4,244,877 number of insertions = 43,635 mapped reads with insertion percentage = 1.17% number of deletions = 94,801 mapped reads with deletion percentage = 2.57% homopolymer indels = 42.78% >>>>>>> Coverage mean coverageData = 0.1363X std coverageData = 2.1396X There is a 2.9% of reference with a coverageData >= 1X There is a 2.24% of reference with a coverageData >= 2X There is a 1.71% of reference with a coverageData >= 3X There is a 1.4% of reference with a coverageData >= 4X There is a 1.07% of reference with a coverageData >= 5X There is a 0.87% of reference with a coverageData >= 6X There is a 0.65% of reference with a coverageData >= 7X There is a 0.53% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.15% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% 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% 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 41181288 0.1652204028009222 1.3949269150651433 chr2 243199373 31436485 0.12926219591857255 5.955811277163566 chr3 198022430 27800000 0.14038813683884194 1.0844476733112471 chr4 191154276 22501681 0.11771476668405785 1.2016431955824398 chr5 180915260 18432376 0.10188403123097521 0.9167245608974391 chr6 171115067 20486242 0.11972202307585222 1.0236492384364584 chr7 159138663 37623071 0.23641691020113698 2.2950525218475604 chr8 146364022 47959813 0.32767487764171993 1.91905307002054 chr9 141213431 14566176 0.10315007500950812 1.1406057076671812 chr10 135534747 20082063 0.1481691112021628 2.958305556600232 chr11 135006516 17505282 0.12966249717902506 1.0672364289078125 chr12 133851895 16544629 0.12360399529644313 1.0140263173508097 chr13 115169878 8400381 0.07293904574597188 0.7766038292192126 chr14 107349540 14412828 0.1342607336743129 1.0590356672449408 chr15 102531392 10120478 0.09870614065202588 0.8886970787208981 chr16 90354753 10148639 0.11231992411068846 1.2362320888356535 chr17 81195210 10720548 0.13203424192141383 1.0996852992307007 chr18 78077248 7586271 0.09716365771498503 1.3488374086179586 chr19 59128983 5615460 0.09496966995018331 1.050431330188676 chr20 63025520 11549658 0.18325367248060787 1.2245327076513974 chr21 48129895 5204586 0.10813624255776996 0.9833126357733537 chr22 51304566 4514141 0.08798711989884098 0.8080621666308597 chrMT 16571 1177039 71.03005250135779 55.03123540227904 chrX 155270560 15485820 0.09973442486457187 0.9074605355941231 chrY 59373566 787100 0.013256741223863833 0.6028067011770725