BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240197.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 = 1,614,601 number of mapped reads = 1,383,230 (85.67%) number of supplementary alignments = 6,968 (0.43%) number of secondary alignments = 0 number of mapped bases = 88,298,185 bp number of sequenced bases = 88,259,522 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,777 duplication rate = 3.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0033 >>>>>>> ACTG content number of A's = 23,854,881 bp (27.03%) number of C's = 15,433,159 bp (17.49%) number of T's = 28,341,373 bp (32.11%) number of G's = 20,607,921 bp (23.35%) number of N's = 22,188 bp (0.03%) GC percentage = 40.84% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 742,684 number of insertions = 6,284 mapped reads with insertion percentage = 0.45% number of deletions = 22,271 mapped reads with deletion percentage = 1.59% homopolymer indels = 48.39% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.2898X There is a 2.46% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 6974577 0.027982185047394526 0.4840760161503416 chr2 243199373 7046309 0.028973384729902244 0.32684428300969115 chr3 198022430 5728233 0.028927192742761513 0.19195882817339718 chr4 191154276 6351594 0.033227580009771794 0.21140098468190024 chr5 180915260 5343213 0.02953434110533296 0.19698021608454258 chr6 171115067 5275034 0.030827408085577875 0.24684321690399452 chr7 159138663 4744118 0.02981122192788562 0.34922829775410913 chr8 146364022 5245140 0.03583626582767724 0.4037768980153755 chr9 141213431 4029837 0.02853720762581004 0.3077873372198457 chr10 135534747 4465058 0.03294400955350586 0.2616832641630635 chr11 135006516 4161405 0.03082373446330546 0.2628284508906409 chr12 133851895 3881824 0.02900088937851795 0.19876598666260895 chr13 115169878 2486248 0.021587658536896252 0.165278277414624 chr14 107349540 2729101 0.025422568182406742 0.19906852620194554 chr15 102531392 2704263 0.02637497596833563 0.19303016717035446 chr16 90354753 2099495 0.023236132359301564 0.1940814407708451 chr17 81195210 2154910 0.026539866083233235 0.1985955241957769 chr18 78077248 1927015 0.024680877584209934 0.5429034975604996 chr19 59128983 1863653 0.03151843487651394 0.32765405146986504 chr20 63025520 1360021 0.021578893756053104 0.17584335398931333 chr21 48129895 1107718 0.023015175910938514 0.1849563380913256 chr22 51304566 880455 0.017161338037631972 0.14496356375703456 chrMT 16571 52033 3.140003620783296 2.6278868185766213 chrX 155270560 5467754 0.035214363881987676 0.24150587298048412 chrY 59373566 219177 0.003691491260605772 0.08311502985945958