BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6003992.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 = 3,173,147
number of mapped reads = 2,247,197 (70.82%)
number of supplementary alignments = 15,653 (0.49%)
number of secondary alignments = 0
number of mapped bases = 147,722,190 bp
number of sequenced bases = 147,659,815 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 82,282
duplication rate = 2.58%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.1774
>>>>>>> ACTG content
number of A's = 41,414,499 bp (28.05%)
number of C's = 25,583,548 bp (17.33%)
number of T's = 47,700,164 bp (32.3%)
number of G's = 32,947,148 bp (22.31%)
number of N's = 14,456 bp (0.01%)
GC percentage = 39.64%
>>>>>>> Mismatches and indels
general error rate = 0.0109
number of mismatches = 1,591,307
number of insertions = 13,940
mapped reads with insertion percentage = 0.61%
number of deletions = 38,020
mapped reads with deletion percentage = 1.67%
homopolymer indels = 46.32%
>>>>>>> Coverage
mean coverageData = 0.0477X
std coverageData = 0.4498X
There is a 4.24% of reference with a coverageData >= 1X
There is a 0.37% of reference with a coverageData >= 2X
There is a 0.05% of reference with a coverageData >= 3X
There is a 0.01% 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 9352516 0.03752253840924232 0.6651618447991839
chr2 243199373 15445808 0.06351088742321716 0.5229677262646854
chr3 198022430 12439616 0.06281922709462762 0.2742675879294171
chr4 191154276 9691625 0.050700539913635 0.24790840872536474
chr5 180915260 5143738 0.02843175307599812 0.1909556845132838
chr6 171115067 7321605 0.04278761144978543 0.2528628432426367
chr7 159138663 10319001 0.0648428282949694 0.7731560070074268
chr8 146364022 12065811 0.08243700080884632 0.8284991416093866
chr9 141213431 5283658 0.0374161151852475 0.4244191832483578
chr10 135534747 5543253 0.040899128250853636 0.37829926553551496
chr11 135006516 7971136 0.05904260206225898 0.4378777237730647
chr12 133851895 7394735 0.05524565042579337 0.2655399324136292
chr13 115169878 6389550 0.05547935025163437 0.25420375023168257
chr14 107349540 3904405 0.03637095231148638 0.27922534485403633
chr15 102531392 2839423 0.027693206388927208 0.19253910813461483
chr16 90354753 2807163 0.03106823832499437 0.261204480305846
chr17 81195210 2676144 0.03295938270250179 0.23803345384027064
chr18 78077248 2925843 0.037473695281882886 0.8880085937978971
chr19 59128983 2091491 0.035371672129047106 0.4184796712583327
chr20 63025520 3960589 0.0628410364563434 0.29733842866543775
chr21 48129895 1559625 0.03240449620760652 0.23210848137861587
chr22 51304566 1227376 0.023923328773505267 0.16446788490289987
chrMT 16571 77053 4.649870255265222 3.3973053506976076
chrX 155270560 8948670 0.05763275407778525 0.31804284370548785
chrY 59373566 342356 0.005766135050739583 0.10365397592679935