BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716778.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 = 1,471,565
number of mapped reads = 1,374,659 (93.41%)
number of supplementary alignments = 34,344 (2.33%)
number of secondary alignments = 0
number of mapped bases = 105,181,229 bp
number of sequenced bases = 105,134,606 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 50,980
duplication rate = 2.79%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.3517
>>>>>>> ACTG content
number of A's = 25,411,701 bp (24.17%)
number of C's = 21,513,797 bp (20.46%)
number of T's = 31,455,153 bp (29.92%)
number of G's = 26,749,829 bp (25.44%)
number of N's = 4,126 bp (0%)
GC percentage = 45.91%
>>>>>>> Mismatches and indels
general error rate = 0.007
number of mismatches = 711,020
number of insertions = 9,526
mapped reads with insertion percentage = 0.68%
number of deletions = 22,470
mapped reads with deletion percentage = 1.6%
homopolymer indels = 38.42%
>>>>>>> Coverage
mean coverageData = 0.034X
std coverageData = 0.2745X
There is a 2.96% of reference with a coverageData >= 1X
There is a 0.31% of reference with a coverageData >= 2X
There is a 0.05% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% 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 8547247 0.034291778153684116 0.3661906627142511
chr2 243199373 8857552 0.03642094916091745 0.30550485424701435
chr3 198022430 6803441 0.034356921082121857 0.2051213613169851
chr4 191154276 6633113 0.034700311909318736 0.2976379835661945
chr5 180915260 6147215 0.03397842172075479 0.20522664308989014
chr6 171115067 5892874 0.03443807785786625 0.2160672060118834
chr7 159138663 5729982 0.03600622181926965 0.33880590069821404
chr8 146364022 5300723 0.03621602445442501 0.2698027770131262
chr9 141213431 4325532 0.030631165671486306 0.2513691912865802
chr10 135534747 5219833 0.03851287670164759 0.38953231385000164
chr11 135006516 4780169 0.035406950283792225 0.29177367005262866
chr12 133851895 4698184 0.03509986915015286 0.21104760331915576
chr13 115169878 3137077 0.027238693436837713 0.18437679417590006
chr14 107349540 3146144 0.029307475374370492 0.21101800280005195
chr15 102531392 3073266 0.029973903016941385 0.19339550889830623
chr16 90354753 3345825 0.037029872684174125 0.23372436928310716
chr17 81195210 3015788 0.03714243734328663 0.2424943235012885
chr18 78077248 2756001 0.035298388078432275 0.37917095206122986
chr19 59128983 2303563 0.03895827195269028 0.288935021268641
chr20 63025520 2405069 0.03816024048671078 0.23856619563905235
chr21 48129895 1442623 0.02997353308167408 0.2514396763949796
chr22 51304566 1437913 0.028026998610610993 0.19149441472708809
chrMT 16571 107408 6.481684871160461 4.877253053192638
chrX 155270560 5697016 0.03669089620079943 0.23251899254843697
chrY 59373566 377671 0.00636092836330565 0.2592874912639556