BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716847.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 = 1,639,970
number of mapped reads = 1,525,906 (93.04%)
number of supplementary alignments = 29,175 (1.78%)
number of secondary alignments = 0
number of mapped bases = 121,584,816 bp
number of sequenced bases = 121,529,519 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 57,081
duplication rate = 2.68%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.8769
>>>>>>> ACTG content
number of A's = 30,563,690 bp (25.15%)
number of C's = 25,033,015 bp (20.6%)
number of T's = 37,524,403 bp (30.88%)
number of G's = 28,399,483 bp (23.37%)
number of N's = 8,928 bp (0.01%)
GC percentage = 43.97%
>>>>>>> Mismatches and indels
general error rate = 0.0066
number of mismatches = 778,131
number of insertions = 9,552
mapped reads with insertion percentage = 0.62%
number of deletions = 28,589
mapped reads with deletion percentage = 1.84%
homopolymer indels = 43.92%
>>>>>>> Coverage
mean coverageData = 0.0393X
std coverageData = 0.3532X
There is a 3.44% of reference with a coverageData >= 1X
There is a 0.35% of reference with a coverageData >= 2X
There is a 0.05% 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 9927577 0.039829698157502286 0.6760354196147694
chr2 243199373 10246065 0.04213031009746888 0.39378608638238327
chr3 198022430 8114392 0.040977135771942605 0.22264224540485195
chr4 191154276 7910173 0.041381093666981325 0.2819358603992696
chr5 180915260 7130519 0.03941358512267014 0.22126719922499233
chr6 171115067 6954450 0.040641950016008815 0.24495841691906042
chr7 159138663 6694294 0.04206579264776153 0.43859712329504663
chr8 146364022 6188000 0.04227814947583225 0.42695665391144266
chr9 141213431 5182856 0.03670228790064594 0.31342342727239203
chr10 135534747 5880419 0.043386800286719096 0.37730814368742915
chr11 135006516 5459633 0.04043977403283261 0.3147978068576596
chr12 133851895 5539574 0.04138584664789393 0.2263240052559114
chr13 115169878 3792670 0.03293109331938339 0.19943450552758457
chr14 107349540 3632276 0.03383597172377264 0.2209083470018446
chr15 102531392 3521297 0.03434359888530529 0.204250484537133
chr16 90354753 3591606 0.03975005055904475 0.24185766344399207
chr17 81195210 3311809 0.040788231226940606 0.2549105383370178
chr18 78077248 3285178 0.04207599632610002 0.5163399138959739
chr19 59128983 2457638 0.0415640160765153 0.4532482934098954
chr20 63025520 2643359 0.04194108989501396 0.23657338545718135
chr21 48129895 1584009 0.032911125195681394 0.23345775700975557
chr22 51304566 1450122 0.028264969632527445 0.1864491930044713
chrMT 16571 9059 0.5466779313258101 0.7932278011927516
chrX 155270560 6697130 0.04313200132723164 0.26443952389393854
chrY 59373566 380711 0.006412129599896358 0.23342895810763822