BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6230382.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 = 3,303,771
number of mapped reads = 2,772,076 (83.91%)
number of supplementary alignments = 13,069 (0.4%)
number of secondary alignments = 0
number of mapped bases = 182,133,298 bp
number of sequenced bases = 182,056,106 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 130,962
duplication rate = 3.54%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.6968
>>>>>>> ACTG content
number of A's = 49,078,339 bp (26.96%)
number of C's = 31,733,720 bp (17.43%)
number of T's = 60,338,711 bp (33.14%)
number of G's = 40,557,044 bp (22.28%)
number of N's = 348,292 bp (0.19%)
GC percentage = 39.71%
>>>>>>> Mismatches and indels
general error rate = 0.0098
number of mismatches = 1,745,228
number of insertions = 16,572
mapped reads with insertion percentage = 0.59%
number of deletions = 46,707
mapped reads with deletion percentage = 1.67%
homopolymer indels = 48.21%
>>>>>>> Coverage
mean coverageData = 0.0588X
std coverageData = 0.4908X
There is a 4.88% of reference with a coverageData >= 1X
There is a 0.71% of reference with a coverageData >= 2X
There is a 0.13% of reference with a coverageData >= 3X
There is a 0.03% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% 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 14465764 0.05803702290474935 0.7526538829150846
chr2 243199373 7857496 0.032308866191032494 0.5271929818788197
chr3 198022430 11023363 0.05566724436216645 0.2748935076943647
chr4 191154276 13785670 0.07211803098770336 0.343321406824661
chr5 180915260 14469410 0.07997893599467508 0.3304039611772034
chr6 171115067 9739485 0.05691775230991202 0.3809138531370901
chr7 159138663 8487088 0.05333140193593307 0.47476470681064564
chr8 146364022 11343769 0.07750380759555787 0.8257689012230714
chr9 141213431 9912068 0.0701921051688065 0.6139124002967603
chr10 135534747 5759615 0.04249548641574548 0.44409652494696616
chr11 135006516 7954846 0.05892194121948899 0.4490269252939386
chr12 133851895 8697545 0.06497887086320295 0.30974932929143834
chr13 115169878 7058908 0.06129126923274157 0.2851877670075721
chr14 107349540 4733832 0.04409736641628832 0.2945882898582663
chr15 102531392 6606495 0.06443387601721041 0.2955121114498717
chr16 90354753 5349061 0.05920065987010113 0.35523038615562835
chr17 81195210 5470077 0.06736945442963939 0.33512936135792837
chr18 78077248 5374268 0.06883270271001354 1.095843563538066
chr19 59128983 3322354 0.05618824866309641 0.5472333154807221
chr20 63025520 4250043 0.06743368400609785 0.3320395777711359
chr21 48129895 3136266 0.06516253567559206 0.3496650042610401
chr22 51304566 2275580 0.04435433680503213 0.24417881592773016
chrMT 16571 49071 2.9612576187315187 2.5988545015495483
chrX 155270560 10527867 0.0678033685200852 0.3659971077688721
chrY 59373566 483357 0.008140946090386418 0.18493993184824947