BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524952.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 = 2,308,270 number of mapped reads = 2,138,672 (92.65%) number of supplementary alignments = 5,310 (0.23%) number of secondary alignments = 0 number of mapped bases = 124,472,478 bp number of sequenced bases = 124,431,810 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,697 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5892 >>>>>>> ACTG content number of A's = 31,013,319 bp (24.92%) number of C's = 22,944,910 bp (18.44%) number of T's = 39,721,523 bp (31.92%) number of G's = 30,750,630 bp (24.71%) number of N's = 1,428 bp (0%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 596,278 number of insertions = 7,997 mapped reads with insertion percentage = 0.37% number of deletions = 23,879 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.66% >>>>>>> Coverage mean coverageData = 0.0402X std coverageData = 0.3417X There is a 3.55% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 13149677 0.05275684749447425 0.6531748499161726 chr2 243199373 11796293 0.04850461929439267 0.39491241862996995 chr3 198022430 6897196 0.03483037754864436 0.2094492176309181 chr4 191154276 8040627 0.042063547665551565 0.25006705369323934 chr5 180915260 5422619 0.029973253776381274 0.19711208854038345 chr6 171115067 10287586 0.06012086592000691 0.3954219627875207 chr7 159138663 7754233 0.048726267104556485 0.48302301209672976 chr8 146364022 9029721 0.06169358341355227 0.34837771949028346 chr9 141213431 3422012 0.02423290742082458 0.25872966960593036 chr10 135534747 6350086 0.04685208878576355 0.3387995386431048 chr11 135006516 5197371 0.03849718631358504 0.29788081137675365 chr12 133851895 5310545 0.039674783834775 0.22344748693495653 chr13 115169878 2428938 0.021090045784367333 0.16514211170140486 chr14 107349540 2828210 0.02634580455584626 0.18681590143806842 chr15 102531392 2505776 0.024439110316575044 0.20408184906885135 chr16 90354753 3939631 0.043601812513393734 0.24397165305174884 chr17 81195210 3146132 0.03874775371601354 0.3058467846139915 chr18 78077248 2304869 0.02952036680391194 0.3985153406989689 chr19 59128983 2991495 0.05059270172125233 0.3953552328013499 chr20 63025520 2968747 0.04710388744115082 0.24276498306352526 chr21 48129895 1429855 0.02970825097374511 0.2044792120576386 chr22 51304566 1659750 0.032350921748368365 0.1976803082384779 chrMT 16571 33164 2.0013276205419106 1.878867185114672 chrX 155270560 5253578 0.033834990998937595 0.24262782506531333 chrY 59373566 324367 0.005463155101716478 0.1285895671675844