BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716510.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 = 1,710,854
number of mapped reads = 1,522,209 (88.97%)
number of supplementary alignments = 6,955 (0.41%)
number of secondary alignments = 0
number of mapped bases = 87,918,486 bp
number of sequenced bases = 87,893,236 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 63,167
duplication rate = 3.17%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.8
>>>>>>> ACTG content
number of A's = 22,428,499 bp (25.52%)
number of C's = 17,490,608 bp (19.9%)
number of T's = 27,202,357 bp (30.95%)
number of G's = 20,770,568 bp (23.63%)
number of N's = 1,204 bp (0%)
GC percentage = 43.53%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 440,314
number of insertions = 5,773
mapped reads with insertion percentage = 0.38%
number of deletions = 16,112
mapped reads with deletion percentage = 1.05%
homopolymer indels = 42.06%
>>>>>>> Coverage
mean coverageData = 0.0284X
std coverageData = 0.2648X
There is a 2.53% of reference with a coverageData >= 1X
There is a 0.23% 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 7058270 0.028317963548825018 0.4850892828930646
chr2 243199373 7464819 0.03069423620594614 0.3424703074044283
chr3 198022430 5782865 0.029203080681314737 0.18847588372000368
chr4 191154276 5494082 0.028741611827715535 0.2029924251460466
chr5 180915260 5333438 0.02948031028449452 0.19074567203804976
chr6 171115067 5128110 0.029968781182781526 0.22021508043525062
chr7 159138663 4804647 0.03019157575805447 0.3073056112150215
chr8 146364022 4513188 0.030835364718250227 0.24706990704781556
chr9 141213431 3635262 0.02574303289890322 0.2197808917751278
chr10 135534747 4248546 0.03134654466134799 0.25425706136874315
chr11 135006516 3966927 0.02938322621405918 0.23849005268189827
chr12 133851895 3946193 0.029481786567160665 0.1924101997444323
chr13 115169878 2790633 0.024230580499529572 0.1716413165526264
chr14 107349540 2477755 0.02308118879689657 0.17593945277945933
chr15 102531392 2550564 0.02487593263144228 0.18135881557661465
chr16 90354753 2581414 0.028569764337687913 0.1976835135985305
chr17 81195210 2462609 0.03032948618520723 0.20077940144703252
chr18 78077248 2277764 0.029173210613160954 0.36180917420960895
chr19 59128983 1910849 0.03231662212083032 0.34412987626842273
chr20 63025520 1907329 0.03026280465436858 0.1954568534202011
chr21 48129895 1189749 0.024719542812216815 0.19558311938328812
chr22 51304566 1109543 0.021626593625214567 0.16333993857109474
chrMT 16571 4996 0.301490555790236 0.5919299738502243
chrX 155270560 5000306 0.03220382537423707 0.21724977975632107
chrY 59373566 278628 0.0046927954436828 0.12074070804894925