BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1549068.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,204,359
number of mapped reads = 8,849,167 (86.72%)
number of secondary alignments = 0
number of mapped bases = 351,549,901 bp
number of sequenced bases = 351,512,685 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 333,741
duplication rate = 2.53%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.171
>>>>>>> ACTG content
number of A's = 103,171,100 bp (29.35%)
number of C's = 72,469,818 bp (20.62%)
number of T's = 103,521,606 bp (29.45%)
number of G's = 72,343,762 bp (20.58%)
number of N's = 6,399 bp (0%)
GC percentage = 41.2%
>>>>>>> Mismatches and indels
general error rate = 0.0031
number of mismatches = 1,088,125
number of insertions = 8,702
mapped reads with insertion percentage = 0.1%
number of deletions = 29,085
mapped reads with deletion percentage = 0.33%
homopolymer indels = 44.57%
>>>>>>> Coverage
mean coverageData = 0.1136X
std coverageData = 1.0592X
There is a 9.33% of reference with a coverageData >= 1X
There is a 1.48% of reference with a coverageData >= 2X
There is a 0.26% of reference with a coverageData >= 3X
There is a 0.06% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% 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 28928711 0.1160627439319399 2.2542762071022246
chr2 243199373 30323870 0.12468728691993791 0.6447555295749335
chr3 198022430 24296569 0.1226960450894376 0.4113334141044628
chr4 191154276 23698088 0.12397362222752474 0.4821703797732073
chr5 180915260 22208492 0.12275632249043004 0.41729453946759654
chr6 171115067 21242651 0.12414249295767742 0.4906208234937331
chr7 159138663 19632429 0.12336680873082363 0.8584606831840039
chr8 146364022 18802501 0.12846395407199182 2.8823896690194077
chr9 141213431 14952076 0.1058828179027815 0.5764871895173673
chr10 135534747 16799747 0.1239515871158855 0.7156784066696107
chr11 135006516 16266635 0.12048777704922035 0.6037152818255849
chr12 133851895 16108843 0.12034826253300336 0.42578749123961795
chr13 115169878 11776467 0.10225301271917644 0.36383914454282656
chr14 107349540 10902977 0.10156519534224366 0.4335172098045621
chr15 102531392 10186327 0.09934837322797685 0.36016203464883473
chr16 90354753 9731506 0.10770331030621046 0.44672170770489245
chr17 81195210 8954905 0.11028858722084714 0.4286185376578264
chr18 78077248 9493893 0.12159615308162501 1.1862695286228988
chr19 59128983 6586123 0.11138569726457159 1.6357327172355942
chr20 63025520 7268023 0.11531873120602575 0.41505803017811205
chr21 48129895 4640766 0.09642169383498551 0.4626737081228546
chr22 51304566 4008780 0.07813690500763616 0.35460903996482945
chrMT 16571 2897 0.17482348681431417 0.4835028738351541
chrX 155270560 11437549 0.07366205802310496 0.42120011831484694
chrY 59373566 3299076 0.0555647272390545 0.6595267678334042