BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6231853.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 = 5,164,891
number of mapped reads = 4,841,057 (93.73%)
number of supplementary alignments = 19,923 (0.39%)
number of secondary alignments = 0
number of mapped bases = 307,612,599 bp
number of sequenced bases = 307,505,085 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 472,038
duplication rate = 7.91%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.8781
>>>>>>> ACTG content
number of A's = 79,661,550 bp (25.91%)
number of C's = 54,783,649 bp (17.82%)
number of T's = 100,021,197 bp (32.53%)
number of G's = 72,922,671 bp (23.71%)
number of N's = 116,018 bp (0.04%)
GC percentage = 41.53%
>>>>>>> Mismatches and indels
general error rate = 0.006
number of mismatches = 1,805,954
number of insertions = 18,311
mapped reads with insertion percentage = 0.37%
number of deletions = 60,988
mapped reads with deletion percentage = 1.25%
homopolymer indels = 44.43%
>>>>>>> Coverage
mean coverageData = 0.0994X
std coverageData = 0.9866X
There is a 7.6% of reference with a coverageData >= 1X
There is a 1.57% of reference with a coverageData >= 2X
There is a 0.38% of reference with a coverageData >= 3X
There is a 0.11% 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 0.01% 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 33946405 0.1361938632842965 2.4181948871048284
chr2 243199373 27729292 0.11401876434936369 1.000029035089742
chr3 198022430 29992185 0.1514585241681965 0.49539814659837483
chr4 191154276 8543926 0.04469649425995576 0.31216265911843405
chr5 180915260 13993156 0.07734646596423099 0.3623273941221977
chr6 171115067 20796947 0.12153778953901237 0.6939964916670048
chr7 159138663 20017891 0.1257889856721996 1.3741854725935008
chr8 146364022 20282146 0.13857330321245204 0.8876499098676855
chr9 141213431 13005343 0.09209706830223535 0.7066491924763538
chr10 135534747 15695007 0.11580061458335847 0.8869229554729566
chr11 135006516 11182682 0.08283068352049022 0.7300189764995862
chr12 133851895 9351380 0.0698636354756128 0.35822496962195427
chr13 115169878 7789146 0.06763179865485314 0.3240537289157987
chr14 107349540 14476826 0.13485689831554007 0.5114956162190422
chr15 102531392 5727065 0.055856698014984524 0.34053473440996634
chr16 90354753 6088935 0.06738920530279133 0.4260656118227652
chr17 81195210 6918469 0.08520784662050877 0.4355924801645766
chr18 78077248 7492202 0.095958838098392 1.6119176528716408
chr19 59128983 7826826 0.132368689649203 1.2752837717549572
chr20 63025520 7278459 0.11548431492512874 0.4639664307067929
chr21 48129895 4753595 0.09876595409152669 0.42789136956155366
chr22 51304566 3329480 0.06489636809324145 0.31231255170546235
chrMT 16571 206321 12.450727173978638 7.809484596998378
chrX 155270560 10515424 0.06772323098467604 0.4854893984172941
chrY 59373566 673491 0.011343280273918531 0.21912278043895897