BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524695.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 = 1,806,431
number of mapped reads = 1,664,973 (92.17%)
number of supplementary alignments = 6,393 (0.35%)
number of secondary alignments = 0
number of mapped bases = 98,313,263 bp
number of sequenced bases = 98,283,892 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 71,391
duplication rate = 3.16%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.7563
>>>>>>> ACTG content
number of A's = 24,852,063 bp (25.29%)
number of C's = 19,194,593 bp (19.53%)
number of T's = 30,627,185 bp (31.16%)
number of G's = 23,596,753 bp (24.01%)
number of N's = 13,298 bp (0.01%)
GC percentage = 43.54%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 489,409
number of insertions = 6,037
mapped reads with insertion percentage = 0.36%
number of deletions = 18,196
mapped reads with deletion percentage = 1.08%
homopolymer indels = 44.01%
>>>>>>> Coverage
mean coverageData = 0.0318X
std coverageData = 0.3078X
There is a 2.83% 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 7973593 0.03199026332616439 0.5603934485274654
chr2 243199373 8198724 0.03371194546624098 0.4364121055582693
chr3 198022430 6530592 0.03297905191851246 0.19847140322610735
chr4 191154276 6333308 0.03313191905788181 0.22774530218304262
chr5 180915260 5899204 0.03260755339267677 0.1987579940400761
chr6 171115067 5574055 0.03257489301044425 0.22998543189261805
chr7 159138663 5459768 0.0343082434970564 0.3477008655439892
chr8 146364022 5019195 0.03429254629255815 0.3374563592860038
chr9 141213431 4134753 0.029280168116586586 0.24497801457195284
chr10 135534747 4796571 0.03538997272780536 0.3190736557409989
chr11 135006516 4451264 0.0329707345384722 0.2542472892114577
chr12 133851895 4446301 0.03321806538487931 0.20330033360998617
chr13 115169878 3078418 0.026729367552164984 0.18043284768959264
chr14 107349540 2929543 0.027289758297986185 0.1880978237187241
chr15 102531392 2832712 0.02762775326409301 0.183455702993465
chr16 90354753 2869762 0.03176105190614599 0.2119697553820338
chr17 81195210 2689688 0.033126190572079314 0.2142940827913429
chr18 78077248 2632552 0.03371727446131298 0.46301716799744624
chr19 59128983 2067600 0.034967623238167315 0.42533512974824755
chr20 63025520 2107427 0.03343767730912811 0.20458205980605576
chr21 48129895 1318602 0.02739673543854604 0.2041624518872066
chr22 51304566 1200256 0.023394720851941327 0.16794433128189926
chrMT 16571 7510 0.4532013758976525 0.7590087225873291
chrX 155270560 5432976 0.034990380661987695 0.2247613482223903
chrY 59373566 328889 0.005539316941145156 0.1910081340181702