BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6008808.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,357,718
number of mapped reads = 1,069,032 (78.74%)
number of supplementary alignments = 11,956 (0.88%)
number of secondary alignments = 0
number of mapped bases = 71,458,347 bp
number of sequenced bases = 71,423,908 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 98,059
duplication rate = 6.86%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.0875
>>>>>>> ACTG content
number of A's = 19,596,644 bp (27.44%)
number of C's = 13,848,791 bp (19.39%)
number of T's = 21,937,213 bp (30.71%)
number of G's = 15,944,375 bp (22.32%)
number of N's = 96,885 bp (0.14%)
GC percentage = 41.71%
>>>>>>> Mismatches and indels
general error rate = 0.0088
number of mismatches = 614,270
number of insertions = 5,358
mapped reads with insertion percentage = 0.5%
number of deletions = 18,952
mapped reads with deletion percentage = 1.75%
homopolymer indels = 44.97%
>>>>>>> Coverage
mean coverageData = 0.0231X
std coverageData = 0.4623X
There is a 1.43% of reference with a coverageData >= 1X
There is a 0.47% of reference with a coverageData >= 2X
There is a 0.19% of reference with a coverageData >= 3X
There is a 0.08% of reference with a coverageData >= 4X
There is a 0.04% of reference with a coverageData >= 5X
There is a 0.02% 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% 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 5624497 0.022565628833478412 1.2154592726234996
chr2 243199373 5881027 0.024181916784793686 0.3136524523121627
chr3 198022430 3229284 0.016307667772787155 0.2003784559580485
chr4 191154276 2029175 0.01061537854376849 0.17411027741249105
chr5 180915260 2970762 0.016420737532035715 0.1885902826712791
chr6 171115067 8848947 0.0517134297706233 0.503761866918467
chr7 159138663 2866216 0.018010808599039193 0.5262108339766394
chr8 146364022 13553252 0.09259961440523956 0.5750360679606971
chr9 141213431 1615620 0.011440979718140266 0.1670911635254177
chr10 135534747 2595279 0.01914844021511325 0.43927187413873675
chr11 135006516 1590799 0.011783127564005874 0.16128808582653328
chr12 133851895 4804666 0.035895390199742784 0.28808300504430034
chr13 115169878 1067746 0.009271052627146135 0.1406798774488244
chr14 107349540 1300832 0.012117723094109207 0.17021323070893524
chr15 102531392 1522662 0.014850690801115818 0.18181650645361616
chr16 90354753 832119 0.009209465715655268 0.17260642838040813
chr17 81195210 989634 0.012188329828816256 0.16254579959930973
chr18 78077248 1152628 0.014762661716765426 0.32880972430788263
chr19 59128983 1259866 0.021307080488768088 0.6747746879682991
chr20 63025520 867308 0.013761219264831134 0.1867696200988583
chr21 48129895 3266738 0.06787336643888378 0.4027057449131124
chr22 51304566 762758 0.014867253725526107 0.18155942197966504
chrMT 16571 82840 4.99909480417597 4.183310057348903
chrX 155270560 2486877 0.016016410322729564 0.18748602960114208
chrY 59373566 256815 0.004325409728632435 0.1130767130804431