BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716593.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 = 1,504,531 number of mapped reads = 1,350,036 (89.73%) number of supplementary alignments = 7,301 (0.49%) number of secondary alignments = 0 number of mapped bases = 78,591,221 bp number of sequenced bases = 78,568,832 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,088 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9539 >>>>>>> ACTG content number of A's = 18,864,610 bp (24.01%) number of C's = 15,716,841 bp (20%) number of T's = 25,461,134 bp (32.41%) number of G's = 18,525,206 bp (23.58%) number of N's = 1,041 bp (0%) GC percentage = 43.58% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 390,730 number of insertions = 5,542 mapped reads with insertion percentage = 0.41% number of deletions = 14,128 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.1% >>>>>>> Coverage mean coverageData = 0.0254X std coverageData = 0.2354X There is a 2.28% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% 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 6420333 0.025758543646717733 0.40983075723290785 chr2 243199373 6741351 0.02771944235234521 0.30153477808223994 chr3 198022430 5037241 0.025437729453173564 0.17325428573252355 chr4 191154276 4971498 0.026007778136231702 0.1852002144329547 chr5 180915260 4766393 0.02634599756814323 0.17755685317823316 chr6 171115067 4597363 0.026867084708560467 0.20392416573522756 chr7 159138663 4222953 0.026536310663864256 0.2770679485981174 chr8 146364022 3948415 0.026976677369524596 0.21850922881078594 chr9 141213431 3260731 0.023090799344716723 0.19950112506850298 chr10 135534747 3759463 0.027738001384988012 0.226936477353549 chr11 135006516 3639530 0.026958180299979 0.2083256981409902 chr12 133851895 3510410 0.02622607621655263 0.17953639305923022 chr13 115169878 2465216 0.021405041342494085 0.15948926765159657 chr14 107349540 2393547 0.022296760656822564 0.1702930755491181 chr15 102531392 2306167 0.022492301674788537 0.1659481251296106 chr16 90354753 2286431 0.025305043996966047 0.18261534615488725 chr17 81195210 2222360 0.027370580111807086 0.19155890052474048 chr18 78077248 2052061 0.02628244530340004 0.32824018575215874 chr19 59128983 1714056 0.02898842349444772 0.3074067866648282 chr20 63025520 1659749 0.026334554637549995 0.18043544020166155 chr21 48129895 1052792 0.021873972507108107 0.17477226437943538 chr22 51304566 950778 0.018532034751059 0.1483198667691801 chrMT 16571 19152 1.155754028121417 1.2322053022137458 chrX 155270560 4358757 0.02807201184822158 0.19642185928989678 chrY 59373566 234474 0.003949131167226843 0.10506515574327123