BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716168.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 = 1,401,143
number of mapped reads = 1,263,854 (90.2%)
number of supplementary alignments = 6,337 (0.45%)
number of secondary alignments = 0
number of mapped bases = 72,876,281 bp
number of sequenced bases = 72,856,004 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 42,100
duplication rate = 2.46%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.1337
>>>>>>> ACTG content
number of A's = 19,199,462 bp (26.35%)
number of C's = 13,575,552 bp (18.63%)
number of T's = 23,200,239 bp (31.84%)
number of G's = 16,879,547 bp (23.17%)
number of N's = 1,204 bp (0%)
GC percentage = 41.8%
>>>>>>> Mismatches and indels
general error rate = 0.0055
number of mismatches = 389,228
number of insertions = 5,243
mapped reads with insertion percentage = 0.41%
number of deletions = 12,158
mapped reads with deletion percentage = 0.95%
homopolymer indels = 42.58%
>>>>>>> Coverage
mean coverageData = 0.0235X
std coverageData = 0.2386X
There is a 2.14% of reference with a coverageData >= 1X
There is a 0.15% 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 5149359 0.020659362770454243 0.38207601022769844
chr2 243199373 6065018 0.024938460676047877 0.26621815563453727
chr3 198022430 4405763 0.022248807874946288 0.15909221640481985
chr4 191154276 4520106 0.023646376605250517 0.18042165237895064
chr5 180915260 3996599 0.022090999952132286 0.16118357387904253
chr6 171115067 3839496 0.022438094244500398 0.17392921501698808
chr7 159138663 4675172 0.029377977116723672 0.32857350831006227
chr8 146364022 3144527 0.021484289356300965 0.2314853877553835
chr9 141213431 3359837 0.02379261644028747 0.2502841973127439
chr10 135534747 2701001 0.019928476348577976 0.22910939075015585
chr11 135006516 2810200 0.02081529161155451 0.20064808592892017
chr12 133851895 5359132 0.04003777458660559 0.23524741826862505
chr13 115169878 3153348 0.027379971697113373 0.17613372556109802
chr14 107349540 2579326 0.024027359595579077 0.18459515174310903
chr15 102531392 1805946 0.017613590967340033 0.14283874832141633
chr16 90354753 2025026 0.02241194771458232 0.17881414128409306
chr17 81195210 2115499 0.026054480307397442 0.17832385498308878
chr18 78077248 2303215 0.02949918265561819 0.44600996862874037
chr19 59128983 1218356 0.020605055899574665 0.3154372898547591
chr20 63025520 2065504 0.03277250231334863 0.19871207862588433
chr21 48129895 869238 0.018060251326124856 0.16360512547545886
chr22 51304566 673774 0.0131328272029433 0.12111594930813385
chrMT 16571 16136 0.973749321103132 1.1857679194463968
chrX 155270560 3818567 0.02459298787870669 0.20260551939986476
chrY 59373566 206136 0.0034718480611388575 0.08855661914837486