BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524862.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 = 2,199,913
number of mapped reads = 2,021,003 (91.87%)
number of supplementary alignments = 9,852 (0.45%)
number of secondary alignments = 0
number of mapped bases = 117,954,651 bp
number of sequenced bases = 117,920,170 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 69,544
duplication rate = 2.32%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.103
>>>>>>> ACTG content
number of A's = 31,043,171 bp (26.33%)
number of C's = 22,416,768 bp (19.01%)
number of T's = 37,384,747 bp (31.7%)
number of G's = 27,060,470 bp (22.95%)
number of N's = 15,014 bp (0.01%)
GC percentage = 41.96%
>>>>>>> Mismatches and indels
general error rate = 0.0049
number of mismatches = 565,717
number of insertions = 8,541
mapped reads with insertion percentage = 0.42%
number of deletions = 21,978
mapped reads with deletion percentage = 1.08%
homopolymer indels = 43.97%
>>>>>>> Coverage
mean coverageData = 0.0381X
std coverageData = 0.362X
There is a 3.41% of reference with a coverageData >= 1X
There is a 0.28% of reference with a coverageData >= 2X
There is a 0.04% 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 9745740 0.03910016336529007 0.7089206327352626
chr2 243199373 7668666 0.03153242504453332 0.37783630199526885
chr3 198022430 8443468 0.04263894751720802 0.2244942075031388
chr4 191154276 6451093 0.03374809674673456 0.21702056892912275
chr5 180915260 7130101 0.03941127464869464 0.21908590130473934
chr6 171115067 7728163 0.04516354483267099 0.2630781054689096
chr7 159138663 5336368 0.03353281911134317 0.5158585752042075
chr8 146364022 12704451 0.08680036819430939 0.4776265486041964
chr9 141213431 4880703 0.03456259766112474 0.30836996802216127
chr10 135534747 5846091 0.04313352206279619 0.32888534657950685
chr11 135006516 5658640 0.0419138288110479 0.3309212972320138
chr12 133851895 4650144 0.03474096500464188 0.2076118903138726
chr13 115169878 3122043 0.027108155832204668 0.1792654231008785
chr14 107349540 2883868 0.026864279064446852 0.1966409424183758
chr15 102531392 3467818 0.033822012286734586 0.2013762887790847
chr16 90354753 3350582 0.037082520716978776 0.23432416236728212
chr17 81195210 3238772 0.039888707720566276 0.2509667574796733
chr18 78077248 2798281 0.03583990306625561 0.6190911711888765
chr19 59128983 1704185 0.02882148336628756 0.4622560009022227
chr20 63025520 2491514 0.03953182774215905 0.2201004917062581
chr21 48129895 1688079 0.035073398768062966 0.22167830266606553
chr22 51304566 709373 0.013826703065766116 0.12664216162814546
chrMT 16571 4440 0.2679379639128598 0.5267587631093226
chrX 155270560 5967380 0.03843214064533547 0.24934484484398942
chrY 59373566 284688 0.004794861066623487 0.11421027763866286