BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525151.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 = 1,415,070
number of mapped reads = 510,649 (36.09%)
number of supplementary alignments = 1,725 (0.12%)
number of secondary alignments = 0
number of mapped bases = 31,498,938 bp
number of sequenced bases = 31,488,833 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 8,500
duplication rate = 1.26%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.7666
>>>>>>> ACTG content
number of A's = 8,045,958 bp (25.55%)
number of C's = 6,066,595 bp (19.27%)
number of T's = 9,711,599 bp (30.84%)
number of G's = 7,663,969 bp (24.34%)
number of N's = 712 bp (0%)
GC percentage = 43.6%
>>>>>>> Mismatches and indels
general error rate = 0.0049
number of mismatches = 150,164
number of insertions = 2,359
mapped reads with insertion percentage = 0.46%
number of deletions = 6,231
mapped reads with deletion percentage = 1.21%
homopolymer indels = 43.07%
>>>>>>> Coverage
mean coverageData = 0.0102X
std coverageData = 0.127X
There is a 0.97% of reference with a coverageData >= 1X
There is a 0.03% 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 3441300 0.013806585460824188 0.20039592296611686
chr2 243199373 2595619 0.01067280300924131 0.13362040458391494
chr3 198022430 2158104 0.010898280563469502 0.10783652709109774
chr4 191154276 1730134 0.009050982464028166 0.09961072600505157
chr5 180915260 1391510 0.0076915015350280565 0.0901681577554576
chr6 171115067 2066490 0.012076610413272374 0.11955482821416491
chr7 159138663 2324446 0.014606419057322356 0.20256514913227394
chr8 146364022 1888750 0.01290446910511929 0.12608824442783192
chr9 141213431 1046959 0.007414018571647056 0.09915643384921688
chr10 135534747 1691003 0.012476527513641944 0.13960202271416192
chr11 135006516 1476534 0.010936761007890908 0.11626439999475364
chr12 133851895 1428209 0.01067006933297433 0.10684930369057216
chr13 115169878 684182 0.005940633192300508 0.0797371836999926
chr14 107349540 1191492 0.011099181235429608 0.11114724688084512
chr15 102531392 668080 0.006515858089588797 0.08378293406830986
chr16 90354753 891522 0.009866907610272589 0.10667580897368337
chr17 81195210 570697 0.00702870280155689 0.08773870736949026
chr18 78077248 678356 0.008688267291388139 0.15126333969208716
chr19 59128983 509858 0.008622810238424023 0.1590545039415733
chr20 63025520 646748 0.010261684473210218 0.10530080935167506
chr21 48129895 375723 0.007806437142653231 0.09409599676033881
chr22 51304566 266794 0.005200199919827799 0.07386789236197293
chrMT 16571 15102 0.9113511556333354 1.0158242726900848
chrX 155270560 1675983 0.010793952182564421 0.10968742741810181
chrY 59373566 85343 0.0014373905047239373 0.05216384969765931