BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716112.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 = 716,883
number of mapped reads = 640,801 (89.39%)
number of supplementary alignments = 2,506 (0.35%)
number of secondary alignments = 0
number of mapped bases = 37,086,378 bp
number of sequenced bases = 37,074,848 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 9,193
duplication rate = 1.02%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.9421
>>>>>>> ACTG content
number of A's = 9,547,083 bp (25.75%)
number of C's = 7,590,214 bp (20.47%)
number of T's = 11,331,152 bp (30.56%)
number of G's = 8,606,094 bp (23.21%)
number of N's = 305 bp (0%)
GC percentage = 43.69%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 188,550
number of insertions = 2,950
mapped reads with insertion percentage = 0.46%
number of deletions = 7,296
mapped reads with deletion percentage = 1.13%
homopolymer indels = 40.72%
>>>>>>> Coverage
mean coverageData = 0.012X
std coverageData = 0.1317X
There is a 1.14% of reference with a coverageData >= 1X
There is a 0.04% 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 3107276 0.012466472450634336 0.16210934620776793
chr2 243199373 2956122 0.012155138245360526 0.15930275226877982
chr3 198022430 2165947 0.010937887187830187 0.11108038539430466
chr4 191154276 2303588 0.012050936281435838 0.1164741199902437
chr5 180915260 2133764 0.011794273186242 0.11213129338287711
chr6 171115067 2001253 0.011695364032437892 0.11991224602016735
chr7 159138663 2131389 0.0133932820586786 0.1726577771428471
chr8 146364022 1943657 0.013279609110495747 0.1342918096784116
chr9 141213431 1235785 0.008751185997314944 0.10482598051839542
chr10 135534747 1641651 0.012112399486753017 0.15779413818760898
chr11 135006516 1301402 0.009639549545890067 0.11317896307024951
chr12 133851895 1848432 0.01380953179631861 0.12151976451296274
chr13 115169878 1136611 0.009868995432989866 0.10244752559661356
chr14 107349540 1247763 0.011623366061931891 0.11344571693375659
chr15 102531392 1365215 0.013315092805918406 0.11993129296312396
chr16 90354753 1280029 0.014166703549065095 0.1274590914158552
chr17 81195210 1616369 0.01990719649595093 0.148886230230955
chr18 78077248 700048 0.008966094706616709 0.14376117613534714
chr19 59128983 921979 0.015592674746325334 0.16116932766753658
chr20 63025520 1070864 0.01699095858312633 0.13724224744562166
chr21 48129895 468811 0.009740536521012564 0.10539886335948995
chr22 51304566 340949 0.006645587841051029 0.08461297655199912
chrMT 16571 1027 0.061975740751915996 0.24111148523072742
chrX 155270560 2052848 0.013221102570893027 0.12190523544961314
chrY 59373566 113599 0.0019132925248249364 0.06530034946589612