BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008798.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,682,607 number of mapped reads = 1,449,688 (86.16%) number of supplementary alignments = 14,400 (0.86%) number of secondary alignments = 0 number of mapped bases = 95,032,854 bp number of sequenced bases = 94,998,102 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 187,301 duplication rate = 9.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6441 >>>>>>> ACTG content number of A's = 26,226,509 bp (27.61%) number of C's = 17,090,227 bp (17.99%) number of T's = 30,714,991 bp (32.33%) number of G's = 20,921,555 bp (22.02%) number of N's = 44,820 bp (0.05%) GC percentage = 40.01% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 766,965 number of insertions = 7,246 mapped reads with insertion percentage = 0.5% number of deletions = 20,234 mapped reads with deletion percentage = 1.38% homopolymer indels = 48.16% >>>>>>> Coverage mean coverageData = 0.0307X std coverageData = 0.4023X There is a 1.75% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 8103233 0.03251038239138429 0.6121126100646688 chr2 243199373 8758883 0.036015236766255974 0.41889173059006285 chr3 198022430 8448152 0.042662601403285476 0.3287010667727623 chr4 191154276 4818787 0.025208889389427 0.2657622272993544 chr5 180915260 4213107 0.023287737032243714 0.23993648719799962 chr6 171115067 4335129 0.025334583774554463 0.2618492344446972 chr7 159138663 5347940 0.03360553556994506 0.413891504223624 chr8 146364022 8547701 0.058400287742844344 0.9325259654888103 chr9 141213431 2689444 0.019045242233368013 0.30850294374975906 chr10 135534747 5808073 0.04285301834812884 0.3926605735532931 chr11 135006516 3668100 0.027169799715444847 0.36374289403254423 chr12 133851895 3988963 0.029801318838257762 0.2729512724632373 chr13 115169878 1814813 0.01575770532638751 0.19656420508214612 chr14 107349540 3118984 0.029054470098334843 0.27393307059517535 chr15 102531392 2120087 0.02067744286549821 0.22093523994817438 chr16 90354753 2124017 0.023507529260801588 0.2469231987981288 chr17 81195210 2579130 0.031764558525065704 0.32242288033053157 chr18 78077248 1620147 0.020750564876466957 0.4789504310506286 chr19 59128983 2168858 0.036680116754248926 0.42570008374135154 chr20 63025520 2337628 0.03709018188187896 0.30510680399893425 chr21 48129895 910995 0.018927841001938606 0.22060102807007864 chr22 51304566 1238054 0.0241314583968998 0.23732225770573076 chrMT 16571 14349 0.8659103252670328 1.7677306513110964 chrX 155270560 5918174 0.0381152357536419 0.3361710063648981 chrY 59373566 340106 0.005728239398657645 0.1930742731948013