BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524909.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 = 1,113,438
number of mapped reads = 1,034,677 (92.93%)
number of supplementary alignments = 4,127 (0.37%)
number of secondary alignments = 0
number of mapped bases = 60,580,116 bp
number of sequenced bases = 60,560,137 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 41,228
duplication rate = 3.13%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.0638
>>>>>>> ACTG content
number of A's = 14,509,406 bp (23.96%)
number of C's = 11,378,229 bp (18.79%)
number of T's = 19,395,517 bp (32.03%)
number of G's = 15,276,497 bp (25.23%)
number of N's = 488 bp (0%)
GC percentage = 44.01%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 299,591
number of insertions = 3,407
mapped reads with insertion percentage = 0.33%
number of deletions = 11,691
mapped reads with deletion percentage = 1.12%
homopolymer indels = 45.03%
>>>>>>> Coverage
mean coverageData = 0.0196X
std coverageData = 0.2008X
There is a 1.77% of reference with a coverageData >= 1X
There is a 0.14% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 5995409 0.024053737462904855 0.3435149167212461
chr2 243199373 5006340 0.020585332676823966 0.23226651192140216
chr3 198022430 3818222 0.01928176520205312 0.15054588395540092
chr4 191154276 2758921 0.014432954667464514 0.1515897774382351
chr5 180915260 3774830 0.020865182959137887 0.1563595554226284
chr6 171115067 4026518 0.02353105469081808 0.17325507398194345
chr7 159138663 3772809 0.023707683154281622 0.24064218157143694
chr8 146364022 4889911 0.033409241787575365 0.26888443793374806
chr9 141213431 2213520 0.01567499624026556 0.16491576523542836
chr10 135534747 2406168 0.0177531448817328 0.20734480559809518
chr11 135006516 3852474 0.02853546713256418 0.20333315944645097
chr12 133851895 2045704 0.015283339843638374 0.1362646037502486
chr13 115169878 1501274 0.01303530077543366 0.12315721896742178
chr14 107349540 1132252 0.010547339094326813 0.11510225923963519
chr15 102531392 1535574 0.014976622964408793 0.13236201594992122
chr16 90354753 1820692 0.020150483948531184 0.158948082399888
chr17 81195210 1384642 0.017053247352891876 0.14737509811205837
chr18 78077248 1621438 0.02076709978302514 0.2636677766184908
chr19 59128983 1239368 0.02096041462441524 0.25064557750424193
chr20 63025520 1160036 0.018405814025810496 0.15067277492581047
chr21 48129895 539201 0.011203037114458695 0.13391887596780047
chr22 51304566 1122015 0.021869690896517864 0.16092147026724377
chrMT 16571 9347 0.5640576911471848 0.8587132952664054
chrX 155270560 2773613 0.017863096520035735 0.15433296624566828
chrY 59373566 179838 0.003028923679605163 0.11365414269084195