BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6231827.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 553,299
number of mapped reads = 371,708 (67.18%)
number of supplementary alignments = 832 (0.15%)
number of secondary alignments = 0
number of mapped bases = 23,190,498 bp
number of sequenced bases = 23,178,754 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 13,987
duplication rate = 2.26%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.5293
>>>>>>> ACTG content
number of A's = 6,256,267 bp (26.99%)
number of C's = 3,833,551 bp (16.54%)
number of T's = 7,567,647 bp (32.65%)
number of G's = 5,520,278 bp (23.82%)
number of N's = 1,011 bp (0%)
GC percentage = 40.36%
>>>>>>> Mismatches and indels
general error rate = 0.0097
number of mismatches = 220,572
number of insertions = 1,854
mapped reads with insertion percentage = 0.49%
number of deletions = 6,836
mapped reads with deletion percentage = 1.82%
homopolymer indels = 48.72%
>>>>>>> Coverage
mean coverageData = 0.0075X
std coverageData = 0.5646X
There is a 0.7% of reference with a coverageData >= 1X
There is a 0.03% of reference with a coverageData >= 2X
There is a 0% 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 1989071 0.007980204791545936 0.1047408085734868
chr2 243199373 2001518 0.008229947204674742 0.10822351570610422
chr3 198022430 1721813 0.008695040253773273 0.0975348696395466
chr4 191154276 1472079 0.007700999584231116 0.09264849947849438
chr5 180915260 1461122 0.008076278363693588 0.09407363611299441
chr6 171115067 1436985 0.008397770139084246 0.1008462487942711
chr7 159138663 1292578 0.008122337938706951 0.12367891764449691
chr8 146364022 1426388 0.009745482397306628 2.5592179789473595
chr9 141213431 939282 0.006651506116298527 0.09425507801557463
chr10 135534747 1070951 0.007901671148580076 0.09892955263640128
chr11 135006516 1055754 0.00782002255357808 0.11071509273876873
chr12 133851895 1070026 0.00799410422990276 0.09393483037540505
chr13 115169878 715776 0.0062149583938953205 0.08229723912122913
chr14 107349540 717446 0.006683270370790597 0.08639502805476076
chr15 102531392 686506 0.006695568904399542 0.08605479893543592
chr16 90354753 606494 0.006712364096662408 0.08671539477827792
chr17 81195210 601364 0.007406397495615813 0.09253950447852892
chr18 78077248 611004 0.007825634428098695 0.1294864163331368
chr19 59128983 411444 0.006958414962083823 0.09621060808852054
chr20 63025520 486188 0.007714145000310985 0.09209340971087293
chr21 48129895 288831 0.006001072722057674 0.08272264908786915
chr22 51304566 235806 0.004596199098536376 0.07127251620889678
chrMT 16571 5343 0.3224307525194617 0.6334972129403897
chrX 155270560 761164 0.0049021784941073185 0.07817909155471561
chrY 59373566 125565 0.002114830023852702 0.04952036158198161