BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6240203.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 = 1,412,521
number of mapped reads = 1,101,010 (77.95%)
number of supplementary alignments = 3,976 (0.28%)
number of secondary alignments = 0
number of mapped bases = 66,536,900 bp
number of sequenced bases = 66,498,006 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 50,096
duplication rate = 3.56%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.3734
>>>>>>> ACTG content
number of A's = 17,688,632 bp (26.6%)
number of C's = 11,208,420 bp (16.86%)
number of T's = 21,233,682 bp (31.93%)
number of G's = 16,352,863 bp (24.59%)
number of N's = 14,409 bp (0.02%)
GC percentage = 41.45%
>>>>>>> Mismatches and indels
general error rate = 0.0103
number of mismatches = 677,409
number of insertions = 4,894
mapped reads with insertion percentage = 0.44%
number of deletions = 22,417
mapped reads with deletion percentage = 2.01%
homopolymer indels = 49.23%
>>>>>>> Coverage
mean coverageData = 0.0215X
std coverageData = 0.2356X
There is a 1.88% of reference with a coverageData >= 1X
There is a 0.19% of reference with a coverageData >= 2X
There is a 0.03% of reference with a coverageData >= 3X
There is a 0.01% 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 4888019 0.01961085986622276 0.30035560907233955
chr2 243199373 6596742 0.02712483144436396 0.29987027089749557
chr3 198022430 4535026 0.022901577361716045 0.17210549822377608
chr4 191154276 4212421 0.022036760506471745 0.17532316291139288
chr5 180915260 3492281 0.019303407573247278 0.1585881837549805
chr6 171115067 3830565 0.022385901295296225 0.20224424865424265
chr7 159138663 4036784 0.025366456673071334 0.4180473182288356
chr8 146364022 3956480 0.02703177970881396 0.3429295605697661
chr9 141213431 2356688 0.016688837480338538 0.21879961206242873
chr10 135534747 2983739 0.0220145687068719 0.19560936469227105
chr11 135006516 3150973 0.023339414225014146 0.23054205350248677
chr12 133851895 3178992 0.02375007092727376 0.17475199486890583
chr13 115169878 1435240 0.012461939049722707 0.12436815138617631
chr14 107349540 2498593 0.023275302344099472 0.17996662144578934
chr15 102531392 1595865 0.015564647751978243 0.17744874614913983
chr16 90354753 2075469 0.022970224931055924 0.17277812918358093
chr17 81195210 1805384 0.022235104755563784 0.1838460663914709
chr18 78077248 1527288 0.01956124273232581 0.3157364022121262
chr19 59128983 1312225 0.022192585318100262 0.24440733933192949
chr20 63025520 1375823 0.021829617589827106 0.17266419326951776
chr21 48129895 1214571 0.02523527217335504 0.18620634790989157
chr22 51304566 600048 0.01169580111056782 0.1192094685166467
chrMT 16571 26163 1.578842556273007 2.278022436233672
chrX 155270560 3699936 0.023828960235604227 0.1957259007369096
chrY 59373566 151585 0.002553072187040273 0.06151423381066279