BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716951.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 = 1,196,325 number of mapped reads = 1,063,241 (88.88%) number of supplementary alignments = 6,746 (0.56%) number of secondary alignments = 0 number of mapped bases = 61,749,687 bp number of sequenced bases = 61,731,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,135 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8351 >>>>>>> ACTG content number of A's = 14,759,029 bp (23.91%) number of C's = 12,428,564 bp (20.13%) number of T's = 19,891,431 bp (32.22%) number of G's = 14,651,744 bp (23.73%) number of N's = 850 bp (0%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 312,686 number of insertions = 4,778 mapped reads with insertion percentage = 0.45% number of deletions = 11,422 mapped reads with deletion percentage = 1.07% homopolymer indels = 39.39% >>>>>>> Coverage mean coverageData = 0.0199X std coverageData = 0.1909X There is a 1.83% of reference with a coverageData >= 1X There is a 0.12% 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 4944833 0.01983879911777632 0.2849466235996292 chr2 243199373 5150832 0.021179462498038596 0.239791013193626 chr3 198022430 4088323 0.020645757149833986 0.15374057301568578 chr4 191154276 3939394 0.020608453456725184 0.1654357389698838 chr5 180915260 3744814 0.02069927102887838 0.15374935292996333 chr6 171115067 3532633 0.020644780509012688 0.16288714709609187 chr7 159138663 3405206 0.02139772909867918 0.25000348280133167 chr8 146364022 3118705 0.021307866218653104 0.1894312707519129 chr9 141213431 2588495 0.01833037397129739 0.16517265802594583 chr10 135534747 2958402 0.02182762771527511 0.19518542736948544 chr11 135006516 2810854 0.020820135822185056 0.18258007006598662 chr12 133851895 2827051 0.0211207394560981 0.15620652113925074 chr13 115169878 1894597 0.016450455908271433 0.13703489383445291 chr14 107349540 1879003 0.017503596196127156 0.14563374395685125 chr15 102531392 1822425 0.017774312475929324 0.14306012036075588 chr16 90354753 1810407 0.020036654850907512 0.1568335497084121 chr17 81195210 1757686 0.021647656308789644 0.16802121346207696 chr18 78077248 1605488 0.020562814918886486 0.252520074315848 chr19 59128983 1310475 0.022162989003210152 0.23708516160959825 chr20 63025520 1330124 0.021104530355322733 0.1582683128661138 chr21 48129895 795517 0.01652854218776085 0.14679821180362274 chr22 51304566 786401 0.015328089901393963 0.1327342303356062 chrMT 16571 17249 1.040914851246153 1.1502192652768006 chrX 155270560 3442755 0.022172619200961214 0.16865345252817315 chrY 59373566 188018 0.0031666954280630544 0.09505377259498907