BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716714.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 = 1,107,248
number of mapped reads = 1,027,129 (92.76%)
number of supplementary alignments = 25,621 (2.31%)
number of secondary alignments = 0
number of mapped bases = 78,343,042 bp
number of sequenced bases = 78,312,993 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 33,294
duplication rate = 2.49%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.0876
>>>>>>> ACTG content
number of A's = 19,789,459 bp (25.27%)
number of C's = 16,584,880 bp (21.18%)
number of T's = 22,779,144 bp (29.09%)
number of G's = 19,156,836 bp (24.46%)
number of N's = 2,674 bp (0%)
GC percentage = 45.64%
>>>>>>> Mismatches and indels
general error rate = 0.0067
number of mismatches = 510,631
number of insertions = 6,657
mapped reads with insertion percentage = 0.64%
number of deletions = 14,344
mapped reads with deletion percentage = 1.38%
homopolymer indels = 39.26%
>>>>>>> Coverage
mean coverageData = 0.0253X
std coverageData = 0.218X
There is a 2.25% of reference with a coverageData >= 1X
There is a 0.2% of reference with a coverageData >= 2X
There is a 0.03% 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 6415125 0.02573764901472402 0.27588319256459687
chr2 243199373 6545217 0.02691296823368044 0.23997878544243764
chr3 198022430 4995765 0.02522827843290278 0.17372436726366958
chr4 191154276 4861678 0.02543326836172893 0.24080241312528672
chr5 180915260 4529530 0.025036749249344695 0.17312187619879071
chr6 171115067 4353320 0.025440892355785363 0.1802393159886712
chr7 159138663 4218101 0.026505821529994884 0.24606814037906846
chr8 146364022 3932992 0.026871303113001364 0.22006712577549714
chr9 141213431 3309180 0.023433889939265054 0.19959274181915126
chr10 135534747 3817575 0.028166762284213363 0.3077201687705475
chr11 135006516 3639227 0.026955935963861182 0.2238372913778176
chr12 133851895 3502508 0.026167040817763543 0.17973556356563097
chr13 115169878 2352125 0.020423091878242677 0.15649906181396947
chr14 107349540 2399685 0.02235393835874844 0.17404848964150035
chr15 102531392 2291712 0.02235132046193228 0.16437794139339548
chr16 90354753 2481558 0.027464609415732675 0.19392134641151818
chr17 81195210 2291601 0.028223352091829062 0.19858419462541957
chr18 78077248 2088191 0.026745192146116627 0.29610500836614106
chr19 59128983 1781341 0.030126359521522636 0.24532430470083633
chr20 63025520 1814194 0.028785069920882842 0.19522717953782442
chr21 48129895 1040815 0.021625125091172544 0.20334380333890964
chr22 51304566 1102793 0.021495026388099647 0.16576988984767388
chrMT 16571 1430 0.08629533522418684 0.2883460752870021
chrX 155270560 4287639 0.027613985548838104 0.1910668228533018
chrY 59373566 289740 0.004879949437431466 0.20432554946495377