BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6063544.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 = 3,556,556
number of mapped reads = 3,192,394 (89.76%)
number of supplementary alignments = 25,789 (0.73%)
number of secondary alignments = 0
number of mapped bases = 207,998,164 bp
number of sequenced bases = 207,906,858 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 211,229
duplication rate = 5.17%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.601
>>>>>>> ACTG content
number of A's = 57,091,823 bp (27.46%)
number of C's = 37,343,456 bp (17.96%)
number of T's = 66,627,311 bp (32.05%)
number of G's = 46,839,886 bp (22.53%)
number of N's = 4,382 bp (0%)
GC percentage = 40.49%
>>>>>>> Mismatches and indels
general error rate = 0.008
number of mismatches = 1,642,159
number of insertions = 15,965
mapped reads with insertion percentage = 0.5%
number of deletions = 56,074
mapped reads with deletion percentage = 1.74%
homopolymer indels = 46.39%
>>>>>>> Coverage
mean coverageData = 0.0672X
std coverageData = 0.5889X
There is a 5.14% of reference with a coverageData >= 1X
There is a 1.08% of reference with a coverageData >= 2X
There is a 0.26% of reference with a coverageData >= 3X
There is a 0.07% of reference with a coverageData >= 4X
There is a 0.03% 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% 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 19087226 0.0765784491265119 1.0418427362027156
chr2 243199373 17633774 0.07250748134124507 0.8556409985967428
chr3 198022430 14435118 0.07289637845571333 0.3365860089563174
chr4 191154276 11270121 0.05895824689791402 0.3271527825703024
chr5 180915260 8099936 0.04477198883057184 0.2661492010939421
chr6 171115067 14288132 0.08350013970423774 0.46734399219653705
chr7 159138663 15925343 0.10007211760978538 0.8925728704489283
chr8 146364022 8477601 0.05792134490537572 0.7774987500482547
chr9 141213431 7453690 0.05278315205017574 0.5183391029335311
chr10 135534747 10187887 0.07516808217452901 0.47529048602249596
chr11 135006516 11480444 0.08503622151096767 0.49637201425615457
chr12 133851895 7041011 0.052602998261623415 0.3070275779363995
chr13 115169878 6446596 0.055974670738124774 0.2994090673493575
chr14 107349540 4455068 0.04150057839092743 0.3044851863669163
chr15 102531392 4252732 0.041477365293158215 0.2705869067781929
chr16 90354753 4644934 0.05140774387375061 0.3184512040697275
chr17 81195210 5943962 0.0732058208852468 0.3876893752680914
chr18 78077248 5719072 0.07324889319869471 0.874652673723376
chr19 59128983 4397556 0.07437225835594027 0.7606497917569813
chr20 63025520 4144387 0.06575728371618354 0.3437259331868172
chr21 48129895 3505656 0.07283739139676079 0.36216819425238705
chr22 51304566 3256217 0.06346836653875992 0.31327168342714407
chrMT 16571 65821 3.9720596222316096 3.1827454437018075
chrX 155270560 15153956 0.0975970976082008 0.466602058351682
chrY 59373566 631924 0.010643187576100785 0.289870520214791