BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524993.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 = 828,698 number of mapped reads = 767,559 (92.62%) number of supplementary alignments = 1,756 (0.21%) number of secondary alignments = 0 number of mapped bases = 44,683,536 bp number of sequenced bases = 44,669,242 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,752 duplication rate = 1.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6865 >>>>>>> ACTG content number of A's = 11,545,063 bp (25.85%) number of C's = 8,230,152 bp (18.42%) number of T's = 14,360,119 bp (32.15%) number of G's = 10,533,442 bp (23.58%) number of N's = 466 bp (0%) GC percentage = 42.01% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 215,936 number of insertions = 3,416 mapped reads with insertion percentage = 0.44% number of deletions = 8,471 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.92% >>>>>>> Coverage mean coverageData = 0.0144X std coverageData = 0.1545X There is a 1.35% of reference with a coverageData >= 1X There is a 0.06% 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 3531459 0.014168305723097878 0.2394709298481114 chr2 243199373 3798411 0.015618506549356934 0.16898148118202397 chr3 198022430 2978228 0.015039851798606854 0.12891573009380675 chr4 191154276 2949903 0.015432053426835192 0.13824005216797816 chr5 180915260 2709373 0.014975922981842438 0.12853885831448228 chr6 171115067 2619874 0.01531059798492204 0.1471256566997169 chr7 159138663 2463532 0.015480411570379977 0.18058455839257642 chr8 146364022 2258102 0.015427985437568804 0.1665212436629235 chr9 141213431 1839157 0.01302395237461513 0.13651210448603573 chr10 135534747 2157041 0.015915040591030136 0.16241384988004187 chr11 135006516 2065683 0.015300617045772813 0.15064026381420276 chr12 133851895 2034643 0.015200703733032693 0.13064096385744686 chr13 115169878 1419612 0.01232624384650299 0.1173360934001839 chr14 107349540 1349457 0.012570682650340188 0.11906258747044482 chr15 102531392 1246996 0.012162089830985616 0.11860331644511718 chr16 90354753 1292836 0.014308444847389488 0.12889291788932153 chr17 81195210 1185672 0.014602733338579948 0.13380416962195044 chr18 78077248 1217411 0.015592391268708651 0.20516945598399766 chr19 59128983 857282 0.014498507440927911 0.16792101209312923 chr20 63025520 957008 0.015184452266320056 0.13100977947693224 chr21 48129895 584000 0.012133830751137106 0.12162610082824009 chr22 51304566 507297 0.009887950323953622 0.10350658620225514 chrMT 16571 1251 0.07549333172409631 0.27471193837644936 chrX 155270560 2528055 0.01628161191664408 0.14143729545373795 chrY 59373566 131253 0.0022106302323158422 0.0706449469252677