BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9867854.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 = 1,800,314
number of mapped reads = 1,667,599 (92.63%)
number of supplementary alignments = 7,524 (0.42%)
number of secondary alignments = 0
number of mapped bases = 99,052,940 bp
number of sequenced bases = 99,022,700 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 73,529
duplication rate = 3.26%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.9512
>>>>>>> ACTG content
number of A's = 24,197,215 bp (24.44%)
number of C's = 18,667,720 bp (18.85%)
number of T's = 31,474,338 bp (31.78%)
number of G's = 24,670,149 bp (24.91%)
number of N's = 13,278 bp (0.01%)
GC percentage = 43.77%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 495,601
number of insertions = 6,805
mapped reads with insertion percentage = 0.41%
number of deletions = 19,017
mapped reads with deletion percentage = 1.13%
homopolymer indels = 43.27%
>>>>>>> Coverage
mean coverageData = 0.032X
std coverageData = 0.3038X
There is a 2.85% of reference with a coverageData >= 1X
There is a 0.25% 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 0.01% 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 8032420 0.03222627878628234 0.532337902553921
chr2 243199373 8342822 0.0343044552174894 0.4107730876923805
chr3 198022430 6561372 0.03313448885563115 0.1988495907159948
chr4 191154276 6392398 0.033441041099180016 0.23028143800246437
chr5 180915260 5966991 0.03298224262563589 0.20068747966850886
chr6 171115067 5645293 0.032991209359722835 0.2321312501557916
chr7 159138663 5473266 0.03439306260855038 0.35130644492103347
chr8 146364022 5044336 0.034464316647434025 0.34344470194000437
chr9 141213431 4160083 0.029459541989316867 0.25576370348812943
chr10 135534747 4787443 0.035322624684576275 0.3127596908346062
chr11 135006516 4550623 0.033706691608870194 0.2694610255561365
chr12 133851895 4443437 0.03319666860151663 0.20164906269958854
chr13 115169878 3106562 0.02697373700439276 0.18556720153002368
chr14 107349540 2989921 0.02785220132289342 0.18884634221684743
chr15 102531392 2830394 0.0276051455538612 0.18178289369821304
chr16 90354753 2900679 0.03210322538317381 0.21728690774402748
chr17 81195210 2668571 0.03286611365374879 0.21521724064653525
chr18 78077248 2646091 0.03389067965100409 0.475332674780757
chr19 59128983 2096119 0.03544994169779649 0.43270149602115454
chr20 63025520 2093264 0.03321295881414386 0.20534316128709712
chr21 48129895 1334983 0.02773708523569395 0.21947063067463704
chr22 51304566 1178123 0.022963316754302143 0.16536849183978183
chrMT 16571 15510 0.9359724820469495 1.107004127326887
chrX 155270560 5454154 0.03512677483741928 0.22645302111405868
chrY 59373566 338085 0.0056942006818320465 0.2110407919975404