BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716977.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 = 735,411
number of mapped reads = 617,851 (84.01%)
number of supplementary alignments = 2,295 (0.31%)
number of secondary alignments = 0
number of mapped bases = 34,737,962 bp
number of sequenced bases = 34,727,339 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 10,516
duplication rate = 1.22%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.4267
>>>>>>> ACTG content
number of A's = 8,626,118 bp (24.84%)
number of C's = 6,293,763 bp (18.12%)
number of T's = 11,392,878 bp (32.81%)
number of G's = 8,414,027 bp (24.23%)
number of N's = 553 bp (0%)
GC percentage = 42.35%
>>>>>>> Mismatches and indels
general error rate = 0.0054
number of mismatches = 181,765
number of insertions = 2,472
mapped reads with insertion percentage = 0.4%
number of deletions = 6,763
mapped reads with deletion percentage = 1.08%
homopolymer indels = 41.89%
>>>>>>> Coverage
mean coverageData = 0.0112X
std coverageData = 0.1321X
There is a 1.06% of reference with a coverageData >= 1X
There is a 0.04% of reference with a coverageData >= 2X
There is a 0% of reference with a coverageData >= 3X
There is a 0% 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 2897323 0.01162413553224407 0.161322945023816
chr2 243199373 3437754 0.014135538087920976 0.17705521668395247
chr3 198022430 2310997 0.011670379966552274 0.11244173281308882
chr4 191154276 2020112 0.010567966577948798 0.10828004307801922
chr5 180915260 1898601 0.010494421531937108 0.10601011374173303
chr6 171115067 1983970 0.011594361822036396 0.11718730283434821
chr7 159138663 1702696 0.010699448945351514 0.20158895648002975
chr8 146364022 2868387 0.01959762351980188 0.15823714517277282
chr9 141213431 1432778 0.010146187865090538 0.11322064850795296
chr10 135534747 1568003 0.01156901115549358 0.14164715519987708
chr11 135006516 1167908 0.008650752827367237 0.10784211319137499
chr12 133851895 1616290 0.012075211934803015 0.11516686402181411
chr13 115169878 951791 0.008264235549507138 0.09506237959253465
chr14 107349540 1131863 0.010543715417876966 0.10782635671102242
chr15 102531392 821480 0.008011985246430674 0.0945556449467754
chr16 90354753 1038720 0.01149601947337513 0.11499878402760659
chr17 81195210 1426704 0.017571282837990074 0.1402413819788257
chr18 78077248 825149 0.010568366856372807 0.1472991660831477
chr19 59128983 730368 0.012352115036377337 0.16432268447950849
chr20 63025520 702104 0.011139995354262845 0.11002214430784486
chr21 48129895 359513 0.007469640230879373 0.0903763419401687
chr22 51304566 483042 0.009415185385254014 0.10064597714994097
chrMT 16571 26008 1.5694888660913644 1.644777825625866
chrX 155270560 1258816 0.00810724196525085 0.10016665587335206
chrY 59373566 77585 0.001306726296345414 0.04356926659146846