BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR053615.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 6,074,324
number of mapped reads = 3,184,447 (52.42%)
number of supplementary alignments = 129 (0%)
number of secondary alignments = 0
number of mapped bases = 147,605,627 bp
number of sequenced bases = 147,572,489 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 439,999
duplication rate = 11.75%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9185
>>>>>>> ACTG content
number of A's = 45,318,891 bp (30.71%)
number of C's = 27,930,758 bp (18.93%)
number of T's = 45,035,651 bp (30.52%)
number of G's = 29,282,499 bp (19.84%)
number of N's = 4,690 bp (0%)
GC percentage = 38.77%
>>>>>>> Mismatches and indels
general error rate = 0.0082
number of mismatches = 1,196,436
number of insertions = 7,504
mapped reads with insertion percentage = 0.24%
number of deletions = 23,047
mapped reads with deletion percentage = 0.72%
homopolymer indels = 45.09%
>>>>>>> Coverage
mean coverageData = 0.0477X
std coverageData = 0.4141X
There is a 3.15% of reference with a coverageData >= 1X
There is a 0.86% of reference with a coverageData >= 2X
There is a 0.34% of reference with a coverageData >= 3X
There is a 0.16% of reference with a coverageData >= 4X
There is a 0.09% of reference with a coverageData >= 5X
There is a 0.05% of reference with a coverageData >= 6X
There is a 0.03% of reference with a coverageData >= 7X
There is a 0.02% 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 11574473 0.04643708791401567 0.395609311987892
chr2 243199373 12753219 0.052439358057062097 0.6223651462345965
chr3 198022430 10277175 0.051899044971824654 0.3535273497385232
chr4 191154276 10115293 0.052916906760694174 0.37670637058084216
chr5 180915260 9388099 0.051892245021232596 0.35533414641997074
chr6 171115067 8889289 0.05194918925520451 0.41389833945528165
chr7 159138663 8103081 0.05091836796442106 0.4303691040390853
chr8 146364022 7580248 0.05179037782932748 0.39219404199973035
chr9 141213431 6079828 0.0430541766243184 0.3378186485323595
chr10 135534747 6721814 0.049594765540086926 0.4100004549516347
chr11 135006516 6631426 0.04911930324903725 0.41927505241511154
chr12 133851895 6712561 0.05014916673387403 0.3446129756094108
chr13 115169878 4992486 0.04334888676360324 0.3231117220643377
chr14 107349540 4489112 0.041817710630152674 0.33519129456105345
chr15 102531392 4183350 0.04080067497766928 0.7306750583079734
chr16 90354753 3897787 0.04313870461247346 0.3348411569738956
chr17 81195210 3612856 0.04449592531382085 0.3221413615245768
chr18 78077248 3960277 0.05072254852015276 0.4061606900779003
chr19 59128983 2440559 0.041275172955367756 0.36330229793540575
chr20 63025520 2955735 0.04689743138969738 0.38353646527846635
chr21 48129895 1937471 0.04025504314937733 0.3458193066465683
chr22 51304566 1466936 0.028592698747320074 0.25254286172582113
chrMT 16571 12896 0.7782270231126667 1.8799268431849732
chrX 155270560 8438333 0.05434599450146892 0.40658810723489563
chrY 59373566 391323 0.006590862337626816 0.11664408176174916