BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524641.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 = 608,548
number of mapped reads = 551,973 (90.7%)
number of supplementary alignments = 2,114 (0.35%)
number of secondary alignments = 0
number of mapped bases = 32,196,360 bp
number of sequenced bases = 32,185,600 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 14,106
duplication rate = 2%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9055
>>>>>>> ACTG content
number of A's = 7,964,346 bp (24.75%)
number of C's = 6,025,425 bp (18.72%)
number of T's = 10,382,465 bp (32.26%)
number of G's = 7,813,098 bp (24.28%)
number of N's = 266 bp (0%)
GC percentage = 43%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 164,441
number of insertions = 2,571
mapped reads with insertion percentage = 0.46%
number of deletions = 6,403
mapped reads with deletion percentage = 1.15%
homopolymer indels = 41.13%
>>>>>>> Coverage
mean coverageData = 0.0104X
std coverageData = 0.1293X
There is a 0.98% of reference with a coverageData >= 1X
There is a 0.05% 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 3186407 0.012783948088939767 0.20311416641745095
chr2 243199373 2871665 0.011807863501358616 0.14934374257667615
chr3 198022430 2019416 0.010197915458364994 0.10570990793662234
chr4 191154276 1467728 0.007678237864791474 0.1007517655853009
chr5 180915260 1995899 0.01103223133305615 0.10970669139357357
chr6 171115067 2100978 0.012278159000457861 0.11919995860417017
chr7 159138663 1951776 0.012264624844812225 0.1509941774704829
chr8 146364022 2867599 0.019592239683055443 0.17938876467729578
chr9 141213431 1177375 0.008337556786648714 0.10778008511428475
chr10 135534747 1425541 0.010517900623668114 0.13523471098367257
chr11 135006516 1607099 0.0119038624772748 0.12501841048476128
chr12 133851895 1057666 0.007901763363155971 0.09526988846277096
chr13 115169878 764003 0.006633705038742856 0.08533577229543023
chr14 107349540 593625 0.0055298327314676895 0.07953219568816768
chr15 102531392 841697 0.008209163882218628 0.09533109905815958
chr16 90354753 957057 0.010592215331494514 0.11073264643262537
chr17 81195210 722336 0.008896288340161937 0.09956514814743461
chr18 78077248 842765 0.010793989562746884 0.15101616175417387
chr19 59128983 673509 0.011390505397327737 0.16217427096543816
chr20 63025520 608179 0.009649726015747272 0.10468242397077816
chr21 48129895 301940 0.00627343982362729 0.09172573809238956
chr22 51304566 584837 0.011399316778159667 0.1118410546509057
chrMT 16571 1510 0.0911230462856798 0.31684607240889245
chrX 155270560 1480793 0.009536856181880196 0.1066219027924229
chrY 59373566 94960 0.0015993649429781596 0.06687424398517713