BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6003996.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 = 4,037,076
number of mapped reads = 3,715,720 (92.04%)
number of supplementary alignments = 29,145 (0.72%)
number of secondary alignments = 0
number of mapped bases = 247,095,895 bp
number of sequenced bases = 246,993,374 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 182,005
duplication rate = 3.64%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 41.3976
>>>>>>> ACTG content
number of A's = 66,722,748 bp (27.01%)
number of C's = 47,821,941 bp (19.36%)
number of T's = 75,168,612 bp (30.43%)
number of G's = 57,228,702 bp (23.17%)
number of N's = 51,371 bp (0.02%)
GC percentage = 42.53%
>>>>>>> Mismatches and indels
general error rate = 0.0083
number of mismatches = 2,003,137
number of insertions = 19,142
mapped reads with insertion percentage = 0.51%
number of deletions = 61,960
mapped reads with deletion percentage = 1.65%
homopolymer indels = 45.93%
>>>>>>> Coverage
mean coverageData = 0.0798X
std coverageData = 0.6125X
There is a 6.16% of reference with a coverageData >= 1X
There is a 1.24% of reference with a coverageData >= 2X
There is a 0.3% of reference with a coverageData >= 3X
There is a 0.09% of reference with a coverageData >= 4X
There is a 0.03% 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% 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 30586625 0.12271433819216042 0.9400626942068608
chr2 243199373 6160440 0.02533082188497254 0.8126332680288846
chr3 198022430 16668325 0.08417392413576583 0.3572644296094624
chr4 191154276 17071459 0.08930723056386142 0.4065070408475103
chr5 180915260 4474646 0.024733380699892313 0.20524230931607618
chr6 171115067 11570202 0.06761650042190616 0.3657530625753319
chr7 159138663 10348308 0.06502698844466225 0.9643009273184562
chr8 146364022 21720584 0.1484011145853863 0.6416383024744284
chr9 141213431 15269223 0.10812868784414706 0.7115300231563167
chr10 135534747 5798712 0.042783951188546505 0.6273102991494766
chr11 135006516 10471693 0.07756435252354783 0.542590922121955
chr12 133851895 22131939 0.16534647492289892 0.5226568960564767
chr13 115169878 5536103 0.0480690185327799 0.265677251233644
chr14 107349540 4548552 0.042371415843980326 0.4096551765705344
chr15 102531392 11135174 0.10860258290456058 0.41849698646157324
chr16 90354753 5883101 0.06511114030714023 0.41332756186774927
chr17 81195210 8922549 0.10989009080708086 0.46973469831476844
chr18 78077248 8773830 0.11237370968812835 1.2193374395923728
chr19 59128983 2830229 0.04786534211149886 0.6758298072069036
chr20 63025520 2004381 0.0318026888155782 0.24719458045647363
chr21 48129895 2644358 0.054942110303793514 0.3762001385373065
chr22 51304566 2908417 0.05668924282489789 0.28872632219339506
chrMT 16571 45141 2.7240963128356768 2.5944703408386673
chrX 155270560 18929956 0.12191593821777934 0.504540121149707
chrY 59373566 661948 0.01114886715748217 0.2327025872692314