BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6230360.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 = 3,953,318
number of mapped reads = 3,533,192 (89.37%)
number of supplementary alignments = 25,416 (0.64%)
number of secondary alignments = 0
number of mapped bases = 230,897,654 bp
number of sequenced bases = 230,800,475 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 161,458
duplication rate = 3.24%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.7815
>>>>>>> ACTG content
number of A's = 63,590,969 bp (27.55%)
number of C's = 43,415,551 bp (18.81%)
number of T's = 70,905,036 bp (30.72%)
number of G's = 52,795,638 bp (22.88%)
number of N's = 93,281 bp (0.04%)
GC percentage = 41.69%
>>>>>>> Mismatches and indels
general error rate = 0.0088
number of mismatches = 2,002,659
number of insertions = 20,124
mapped reads with insertion percentage = 0.56%
number of deletions = 58,770
mapped reads with deletion percentage = 1.65%
homopolymer indels = 45.56%
>>>>>>> Coverage
mean coverageData = 0.0746X
std coverageData = 0.5977X
There is a 6.18% of reference with a coverageData >= 1X
There is a 0.89% of reference with a coverageData >= 2X
There is a 0.16% of reference with a coverageData >= 3X
There is a 0.04% of reference with a coverageData >= 4X
There is a 0.02% 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 0.01% 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 16805168 0.06742277284035332 0.9522682674375441
chr2 243199373 20864229 0.08579063647503729 0.872450689968631
chr3 198022430 16513285 0.0833909825265754 0.3362163064180006
chr4 191154276 14493863 0.07582285525226755 0.3723725420401087
chr5 180915260 14566958 0.08051812765821965 0.33234755294999785
chr6 171115067 14411131 0.08421894841089593 0.4674986752991057
chr7 159138663 8458096 0.05314922119208705 0.5642952945190229
chr8 146364022 11591561 0.0791967919547879 0.7374217471009682
chr9 141213431 9635283 0.06823205789823207 0.6557846945447627
chr10 135534747 10957578 0.08084700228200521 0.6094381177583132
chr11 135006516 11160371 0.08266542483030967 0.6510564269428969
chr12 133851895 11089160 0.08284649238623032 0.3479568344371745
chr13 115169878 8173162 0.07096614272700714 0.3085691833026609
chr14 107349540 7379224 0.06874015482506958 0.36520337909982575
chr15 102531392 6487145 0.06326984227425685 0.30554108963878734
chr16 90354753 7102250 0.07860405528417526 0.4499799605567148
chr17 81195210 6576981 0.0810020812804105 0.3854609338457107
chr18 78077248 6961426 0.08916075013299649 1.2893081513572704
chr19 59128983 4666236 0.0789162228614688 0.7385464850304079
chr20 63025520 4875834 0.07736285238106723 0.35545178056407817
chr21 48129895 3111264 0.06464306643511274 0.3529853562254736
chr22 51304566 2741163 0.05342922109505809 0.268449017696671
chrMT 16571 22022 1.3289481624524773 1.5286606081493093
chrX 155270560 11623407 0.07485905248232505 0.399639960304688
chrY 59373566 630857 0.010625216615757929 0.2476458049370341