BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524692.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 = 2,730,947
number of mapped reads = 2,521,092 (92.32%)
number of supplementary alignments = 10,601 (0.39%)
number of secondary alignments = 0
number of mapped bases = 149,229,999 bp
number of sequenced bases = 149,184,437 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 125,657
duplication rate = 3.62%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.8747
>>>>>>> ACTG content
number of A's = 39,147,637 bp (26.24%)
number of C's = 25,358,546 bp (17%)
number of T's = 47,802,954 bp (32.04%)
number of G's = 36,854,743 bp (24.7%)
number of N's = 20,557 bp (0.01%)
GC percentage = 41.7%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 741,710
number of insertions = 11,393
mapped reads with insertion percentage = 0.45%
number of deletions = 28,364
mapped reads with deletion percentage = 1.12%
homopolymer indels = 43.4%
>>>>>>> Coverage
mean coverageData = 0.0482X
std coverageData = 0.4213X
There is a 4.18% of reference with a coverageData >= 1X
There is a 0.46% of reference with a coverageData >= 2X
There is a 0.07% of reference with a coverageData >= 3X
There is a 0.02% 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 11931067 0.047867752353563844 0.7877501101424702
chr2 243199373 12662564 0.05206659804998757 0.5638742253068144
chr3 198022430 10001061 0.050504687777036164 0.2539494967178478
chr4 191154276 9688541 0.05068440634830476 0.30256727469052636
chr5 180915260 9142673 0.05053566515063461 0.255791872057405
chr6 171115067 8651651 0.05056042785525135 0.30071816496668696
chr7 159138663 8247107 0.05182340258821956 0.5228513357851841
chr8 146364022 7565835 0.051691904175740676 0.4525124759459214
chr9 141213431 6275631 0.04444075153163016 0.34118907928282527
chr10 135534747 7160001 0.05282778887689959 0.45540403938009966
chr11 135006516 6819994 0.05051603583341118 0.35568720235976775
chr12 133851895 6662999 0.049778891811729675 0.25534001758545755
chr13 115169878 4756472 0.041299618290817325 0.22998789858882865
chr14 107349540 4420938 0.041182645030430495 0.23709513161580098
chr15 102531392 4229289 0.041248723122768095 0.23351731939053322
chr16 90354753 4259285 0.04713957881108922 0.28179293384888005
chr17 81195210 3934085 0.048452180861407956 0.268283765307205
chr18 78077248 4019040 0.05147517494469067 0.6827802409136379
chr19 59128983 3048431 0.0515556135981571 0.5815367711390501
chr20 63025520 3118628 0.049481987613906236 0.2599165758963444
chr21 48129895 1987631 0.04129722285909828 0.27481183105691914
chr22 51304566 1730935 0.033738420085261026 0.2062778717303936
chrMT 16571 37374 2.2553859151529783 1.7907268803830445
chrX 155270560 8386386 0.054011436553072265 0.29431163026398166
chrY 59373566 492381 0.008292932919003047 0.29354985370426884