BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716328.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 = 990,235
number of mapped reads = 902,219 (91.11%)
number of supplementary alignments = 3,795 (0.38%)
number of secondary alignments = 0
number of mapped bases = 51,347,234 bp
number of sequenced bases = 51,333,697 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 17,047
duplication rate = 1.45%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.9567
>>>>>>> ACTG content
number of A's = 12,566,510 bp (24.48%)
number of C's = 10,789,591 bp (21.02%)
number of T's = 15,252,721 bp (29.71%)
number of G's = 12,723,813 bp (24.79%)
number of N's = 1,062 bp (0%)
GC percentage = 45.81%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 254,885
number of insertions = 3,344
mapped reads with insertion percentage = 0.37%
number of deletions = 8,047
mapped reads with deletion percentage = 0.89%
homopolymer indels = 40.9%
>>>>>>> Coverage
mean coverageData = 0.0166X
std coverageData = 0.1558X
There is a 1.55% of reference with a coverageData >= 1X
There is a 0.08% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% 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 5767209 0.02313819310404045 0.2215234419823048
chr2 243199373 4291365 0.017645460788256226 0.17474576506310976
chr3 198022430 3367454 0.017005417012608118 0.1371999511002108
chr4 191154276 3240830 0.01695400211711717 0.14290495189165403
chr5 180915260 2561605 0.014159142794256271 0.12611310211159796
chr6 171115067 2674414 0.015629330875930405 0.13657195153575438
chr7 159138663 2182878 0.013716830082957276 0.13772981898313352
chr8 146364022 3224182 0.02202851463046021 0.16557987362725707
chr9 141213431 1897950 0.013440293791884429 0.15268369312488267
chr10 135534747 2452236 0.018093042959677345 0.1689591628139185
chr11 135006516 1637023 0.012125511038296849 0.13674408917133624
chr12 133851895 2318124 0.017318574384023476 0.13949596719478358
chr13 115169878 1535389 0.013331515381131167 0.12053440966742228
chr14 107349540 1788310 0.016658757922949647 0.1447911305162744
chr15 102531392 1466839 0.01430624291143926 0.12575648852724106
chr16 90354753 1543356 0.01708107154030956 0.1441157836238095
chr17 81195210 1162392 0.01431601691774675 0.1279262651669243
chr18 78077248 1252075 0.016036361834884345 0.2429136748171852
chr19 59128983 1002935 0.01696181718532179 0.16813243975478154
chr20 63025520 1662495 0.02637812428997016 0.17404253465129665
chr21 48129895 664291 0.013802045485451402 0.13077017422043416
chr22 51304566 622682 0.012136970420917312 0.11548660510699182
chrMT 16571 2364 0.14265886186711726 0.3790381675306623
chrX 155270560 2879946 0.018547920481513044 0.1548898677022752
chrY 59373566 148890 0.0025076816171021293 0.06521388690267833