BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525245.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 = 1,150,769
number of mapped reads = 1,040,833 (90.45%)
number of supplementary alignments = 3,559 (0.31%)
number of secondary alignments = 0
number of mapped bases = 60,074,267 bp
number of sequenced bases = 60,054,731 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 28,335
duplication rate = 1.97%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.135
>>>>>>> ACTG content
number of A's = 15,990,792 bp (26.63%)
number of C's = 10,184,666 bp (16.96%)
number of T's = 19,332,402 bp (32.19%)
number of G's = 14,545,682 bp (24.22%)
number of N's = 1,189 bp (0%)
GC percentage = 41.18%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 298,996
number of insertions = 4,637
mapped reads with insertion percentage = 0.44%
number of deletions = 12,325
mapped reads with deletion percentage = 1.18%
homopolymer indels = 43.72%
>>>>>>> Coverage
mean coverageData = 0.0194X
std coverageData = 0.2035X
There is a 1.8% of reference with a coverageData >= 1X
There is a 0.1% 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 6043639 0.02424723748230902 0.3197616068341405
chr2 243199373 4860947 0.01998749807632111 0.24213748565679227
chr3 198022430 4285647 0.021642230125142894 0.15668242162101745
chr4 191154276 3387508 0.01772132996909784 0.14355146361148954
chr5 180915260 2652983 0.014664230093138633 0.12850869350396046
chr6 171115067 3627651 0.021200067671422528 0.16669841731917737
chr7 159138663 4295046 0.02698933068201032 0.3513561765538449
chr8 146364022 3932730 0.026869513055605972 0.22213175220613904
chr9 141213431 1910116 0.01352644707003826 0.15311675414745982
chr10 135534747 3897471 0.028756249495194026 0.23462991005441383
chr11 135006516 2648804 0.019619823386894896 0.1791574747482361
chr12 133851895 2592975 0.01937197078905756 0.1477598026729331
chr13 115169878 1857408 0.0161275502957466 0.13657865785255244
chr14 107349540 1807062 0.016833439621632286 0.14021344215504114
chr15 102531392 1550324 0.015120481344874358 0.13281120318972603
chr16 90354753 1460577 0.01616491608360658 0.1453851735970496
chr17 81195210 948519 0.011681957593311231 0.11727593830755481
chr18 78077248 1251113 0.016024040703893662 0.2925803003493584
chr19 59128983 1032545 0.01746258683326246 0.23269763286244396
chr20 63025520 1027240 0.01629879452006108 0.13708302387910576
chr21 48129895 805821 0.016742629502931598 0.1393618715172277
chr22 51304566 573874 0.011185632093642503 0.11181537625156886
chrMT 16571 81480 4.91702371613059 3.5784026004477707
chrX 155270560 3379414 0.021764679666254828 0.16587159718414388
chrY 59373566 163373 0.002751611718925557 0.07198039528961589