BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716927.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 = 2,055,137
number of mapped reads = 1,896,636 (92.29%)
number of supplementary alignments = 9,906 (0.48%)
number of secondary alignments = 0
number of mapped bases = 110,901,257 bp
number of sequenced bases = 110,870,189 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 84,375
duplication rate = 3.37%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.6474
>>>>>>> ACTG content
number of A's = 26,552,056 bp (23.95%)
number of C's = 23,086,912 bp (20.82%)
number of T's = 35,020,196 bp (31.59%)
number of G's = 26,209,523 bp (23.64%)
number of N's = 1,502 bp (0%)
GC percentage = 44.46%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 546,934
number of insertions = 6,353
mapped reads with insertion percentage = 0.33%
number of deletions = 19,810
mapped reads with deletion percentage = 1.04%
homopolymer indels = 44.47%
>>>>>>> Coverage
mean coverageData = 0.0358X
std coverageData = 0.3265X
There is a 3.13% of reference with a coverageData >= 1X
There is a 0.33% 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% 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 11300472 0.04533778874717428 0.5735246475360658
chr2 243199373 10074134 0.041423355149850655 0.4083518239397806
chr3 198022430 8148472 0.04114923748789468 0.22672818692082655
chr4 191154276 5436551 0.028440645502484076 0.20910508523367977
chr5 180915260 5197619 0.028729577593399253 0.19069264490771606
chr6 171115067 8442538 0.04933836714682758 0.30785753074746636
chr7 159138663 7249442 0.045554247241602126 0.5900268670842184
chr8 146364022 6954429 0.04751460710747618 0.29519238815736887
chr9 141213431 4380167 0.031018062297487835 0.25441205339345185
chr10 135534747 5703704 0.042082964894603746 0.2980945852165587
chr11 135006516 3920933 0.02904254636124378 0.26900288436993114
chr12 133851895 4722077 0.03527837241303158 0.21252424816477963
chr13 115169878 2404404 0.020877021333651147 0.16254839975891314
chr14 107349540 2580099 0.02403456037166065 0.19353824852664087
chr15 102531392 3551388 0.03463707973456558 0.21227247720618353
chr16 90354753 2542379 0.028137745006065147 0.20254617306482503
chr17 81195210 3446993 0.04245315702736652 0.2440679046687827
chr18 78077248 2259071 0.028933793875521842 0.4511873247327824
chr19 59128983 1954549 0.03305568438408623 0.3779644996324816
chr20 63025520 1868308 0.02964367449883793 0.19707714054057668
chr21 48129895 1105731 0.022973891798434218 0.18206460248265233
chr22 51304566 1974058 0.03847723806882997 0.22073593214099094
chrMT 16571 8600 0.5189789391104942 0.8106176065698942
chrX 155270560 5394846 0.034744809318649976 0.23883041852854076
chrY 59373566 280293 0.004720838226223434 0.11465721968754267