BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524382.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 = 1,382,101
number of mapped reads = 1,286,909 (93.11%)
number of supplementary alignments = 5,166 (0.37%)
number of secondary alignments = 0
number of mapped bases = 75,773,178 bp
number of sequenced bases = 75,751,122 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 47,007
duplication rate = 2.75%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.909
>>>>>>> ACTG content
number of A's = 19,479,277 bp (25.71%)
number of C's = 15,561,681 bp (20.54%)
number of T's = 22,817,245 bp (30.12%)
number of G's = 17,882,697 bp (23.61%)
number of N's = 10,222 bp (0.01%)
GC percentage = 44.15%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 366,669
number of insertions = 5,686
mapped reads with insertion percentage = 0.44%
number of deletions = 14,049
mapped reads with deletion percentage = 1.08%
homopolymer indels = 42.81%
>>>>>>> Coverage
mean coverageData = 0.0245X
std coverageData = 0.253X
There is a 2.22% of reference with a coverageData >= 1X
There is a 0.16% 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 6341234 0.025441196393247902 0.5163809332258902
chr2 243199373 6074405 0.02497705863740035 0.2646427027084952
chr3 198022430 5039232 0.02544778386973637 0.17077575219589267
chr4 191154276 5009767 0.026207977686044544 0.19246631813403897
chr5 180915260 4717708 0.02607689367939443 0.1730959067871216
chr6 171115067 2889391 0.01688566092195727 0.14982411577832183
chr7 159138663 4382835 0.02754098166578162 0.3541732111911199
chr8 146364022 4091440 0.027953864235843423 0.24089823454652334
chr9 141213431 2837547 0.02009403057418809 0.19423815094000166
chr10 135534747 3763061 0.027764548083009297 0.23158469473648027
chr11 135006516 3175487 0.02352099064611074 0.20385888178817485
chr12 133851895 3646260 0.02724100394693702 0.18178091767705273
chr13 115169878 2370656 0.02058399332506022 0.1539104820324958
chr14 107349540 2091671 0.01948467594737714 0.15455629534125107
chr15 102531392 2320143 0.022628611147696112 0.16075367532758233
chr16 90354753 2363377 0.026156642805498013 0.18244199989507429
chr17 81195210 2092121 0.025766556918813313 0.18715241379163514
chr18 78077248 2069956 0.026511641393917984 0.3167194564971646
chr19 59128983 2179660 0.036862802121930625 0.3756384184192986
chr20 63025520 2147827 0.034078687490400716 0.2026532554820152
chr21 48129895 1044552 0.02170276914171535 0.1775557582504395
chr22 51304566 526472 0.01026169873457267 0.10828506800416657
chrMT 16571 3178 0.1917808219178082 0.45206668077409085
chrX 155270560 4357791 0.028065790449908857 0.19548140902742145
chrY 59373566 237407 0.003998530255029654 0.11808912058112646