BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6231840.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 = 11,197,186
number of mapped reads = 8,414,726 (75.15%)
number of supplementary alignments = 62,586 (0.56%)
number of secondary alignments = 0
number of mapped bases = 559,804,592 bp
number of sequenced bases = 559,591,551 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 573,166
duplication rate = 3.17%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.1856
>>>>>>> ACTG content
number of A's = 160,772,546 bp (28.73%)
number of C's = 115,024,057 bp (20.56%)
number of T's = 155,876,894 bp (27.86%)
number of G's = 127,873,187 bp (22.85%)
number of N's = 44,867 bp (0.01%)
GC percentage = 43.41%
>>>>>>> Mismatches and indels
general error rate = 0.0066
number of mismatches = 3,619,022
number of insertions = 44,154
mapped reads with insertion percentage = 0.52%
number of deletions = 125,369
mapped reads with deletion percentage = 1.47%
homopolymer indels = 44.54%
>>>>>>> Coverage
mean coverageData = 0.1808X
std coverageData = 13.4477X
There is a 12.86% of reference with a coverageData >= 1X
There is a 3.04% of reference with a coverageData >= 2X
There is a 0.83% of reference with a coverageData >= 3X
There is a 0.27% of reference with a coverageData >= 4X
There is a 0.1% of reference with a coverageData >= 5X
There is a 0.05% of reference with a coverageData >= 6X
There is a 0.03% of reference with a coverageData >= 7X
There is a 0.02% of reference with a coverageData >= 8X
There is a 0.02% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% 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 67367232 0.2702790939084561 7.6579648544388474
chr2 243199373 49537437 0.2036906443833636 47.01937772251894
chr3 198022430 50322700 0.25412626236330904 0.6547962175847917
chr4 191154276 18200171 0.09521194807067773 0.6949172511354595
chr5 180915260 26541763 0.146708259988682 0.5553736940864924
chr6 171115067 40067720 0.23415658657340793 1.3671952483821397
chr7 159138663 39407806 0.2476318781187699 4.062464425321335
chr8 146364022 38765855 0.2648591810356236 1.9272353718446635
chr9 141213431 21113568 0.14951529645930067 1.536135226129401
chr10 135534747 20245138 0.14937230819488673 1.7351306900138073
chr11 135006516 18330645 0.13577600210052085 1.3144325332675924
chr12 133851895 16720668 0.1249191727916889 0.5500486135242989
chr13 115169878 23167582 0.20116008111079184 0.5658170208568557
chr14 107349540 22003713 0.2049725876794628 0.9316438594712687
chr15 102531392 9759638 0.09518682824475845 0.40267535197931675
chr16 90354753 12852393 0.1422436847345485 1.0110081246844023
chr17 81195210 12962787 0.15964965174669787 0.7685192800038791
chr18 78077248 10289692 0.13178861017232574 4.018142056422114
chr19 59128983 17253306 0.2917910155836775 4.187794487935876
chr20 63025520 10208191 0.16196916741028078 0.698749674367107
chr21 48129895 7785241 0.16175478878563937 0.7008179321858158
chr22 51304566 3937541 0.07674835413284657 0.33680388327596433
chrMT 16571 442927 26.72904471667371 14.205362137590683
chrX 155270560 21002788 0.13526574516122053 0.8382751839310812
chrY 59373566 1518090 0.025568449097364304 0.6181486025935949