BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525156.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 = 1,081,800 number of mapped reads = 979,784 (90.57%) number of supplementary alignments = 3,196 (0.3%) number of secondary alignments = 0 number of mapped bases = 58,924,180 bp number of sequenced bases = 58,905,357 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,707 duplication rate = 1.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3015 >>>>>>> ACTG content number of A's = 14,570,939 bp (24.74%) number of C's = 10,889,599 bp (18.49%) number of T's = 18,805,877 bp (31.93%) number of G's = 14,637,558 bp (24.85%) number of N's = 1,384 bp (0%) GC percentage = 43.34% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 290,300 number of insertions = 4,017 mapped reads with insertion percentage = 0.41% number of deletions = 11,590 mapped reads with deletion percentage = 1.17% homopolymer indels = 42.85% >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 0.201X There is a 1.77% of reference with a coverageData >= 1X There is a 0.09% 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 6772208 0.02717027533504119 0.3362591822898186 chr2 243199373 3758822 0.015455722412573819 0.21197832115007825 chr3 198022430 3218224 0.016251815514030404 0.13560924555275058 chr4 191154276 3312341 0.017328103086744446 0.14356242932806934 chr5 180915260 2661874 0.01471337464844038 0.12744267738982323 chr6 171115067 3390573 0.019814578923082207 0.16200216043690643 chr7 159138663 4410966 0.02771775203364628 0.3621786176454691 chr8 146364022 3468978 0.02370102947840556 0.1845778060808271 chr9 141213431 1959855 0.013878672772988569 0.15241204630040642 chr10 135534747 3980027 0.02936536266969237 0.22933872378403944 chr11 135006516 2729796 0.02021973517189348 0.17176747194300993 chr12 133851895 2678009 0.020007255033632508 0.14886565605869395 chr13 115169878 1820036 0.01580305572608143 0.13295030711088085 chr14 107349540 1881013 0.017522320077011974 0.14370721066438508 chr15 102531392 1624531 0.01584423041871898 0.13283927693303993 chr16 90354753 1631218 0.018053483030383583 0.15397728124342966 chr17 81195210 1088518 0.01340618492149968 0.12499333191240804 chr18 78077248 1284905 0.016456842843641212 0.3029573569174828 chr19 59128983 1217321 0.020587551793339657 0.24436309186879432 chr20 63025520 1116461 0.01771442742558887 0.14187476428696974 chr21 48129895 822932 0.017098146588518427 0.1414814695259501 chr22 51304566 661416 0.012891951956089054 0.11909007791739246 chrMT 16571 44090 2.660672258765313 2.0985050560142917 chrX 155270560 3213804 0.020698089837506865 0.15874696633579 chrY 59373566 176262 0.0029686948565629356 0.08813392631827331