BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716659.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 = 1,011,337
number of mapped reads = 919,636 (90.93%)
number of supplementary alignments = 4,399 (0.43%)
number of secondary alignments = 0
number of mapped bases = 53,519,532 bp
number of sequenced bases = 53,504,082 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 23,712
duplication rate = 1.89%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.8183
>>>>>>> ACTG content
number of A's = 13,366,310 bp (24.98%)
number of C's = 10,047,361 bp (18.78%)
number of T's = 17,177,986 bp (32.11%)
number of G's = 12,910,754 bp (24.13%)
number of N's = 1,671 bp (0%)
GC percentage = 42.91%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 268,558
number of insertions = 3,665
mapped reads with insertion percentage = 0.4%
number of deletions = 9,789
mapped reads with deletion percentage = 1.06%
homopolymer indels = 42.2%
>>>>>>> Coverage
mean coverageData = 0.0173X
std coverageData = 0.1906X
There is a 1.61% of reference with a coverageData >= 1X
There is a 0.09% of reference with a coverageData >= 2X
There is a 0.01% 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 5469635 0.02194431844564993 0.3272436255724025
chr2 243199373 4896751 0.02013471885061151 0.2281021241770969
chr3 198022430 3929816 0.019845307423002535 0.14917697230748622
chr4 191154276 2714233 0.014199174911473076 0.13207935402689552
chr5 180915260 2514385 0.013898136619321112 0.1253776178047641
chr6 171115067 4153078 0.024270673955321537 0.18590240766981342
chr7 159138663 3356717 0.021093032558656095 0.3182759966023906
chr8 146364022 3363857 0.022982813358326543 0.1919983242909991
chr9 141213431 2083195 0.014752102439887605 0.1487012556570324
chr10 135534747 2770446 0.020440854181843125 0.18777621427033003
chr11 135006516 1885807 0.013968266539075787 0.15037762157062276
chr12 133851895 2299057 0.017176125896461905 0.14005530870021013
chr13 115169878 1191939 0.010349398824578072 0.10764891141924926
chr14 107349540 1237983 0.011532261805686358 0.11885164483159416
chr15 102531392 1686656 0.016450142411018862 0.1360896330667481
chr16 90354753 1185093 0.0131160006601977 0.12726214992011503
chr17 81195210 1619573 0.019946656951807872 0.1524864032730557
chr18 78077248 1103121 0.014128584552570295 0.23613814405597366
chr19 59128983 1054340 0.01783118779499387 0.21459746872312782
chr20 63025520 850247 0.013490519395952624 0.12318342558903526
chr21 48129895 562241 0.011681741670119995 0.12221783358245057
chr22 51304566 878761 0.01712831953397676 0.1384641300944138
chrMT 16571 18994 1.1462192987749684 1.1269304677871022
chrX 155270560 2552372 0.01643822241640656 0.14650162639856132
chrY 59373566 141235 0.002378752187463357 0.06792811606574098