BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6238528.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 = 3,348,761
number of mapped reads = 2,927,361 (87.42%)
number of supplementary alignments = 24,643 (0.74%)
number of secondary alignments = 0
number of mapped bases = 179,796,553 bp
number of sequenced bases = 179,708,057 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 896,120
duplication rate = 19.95%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 38.9713
>>>>>>> ACTG content
number of A's = 43,962,722 bp (24.46%)
number of C's = 31,258,801 bp (17.39%)
number of T's = 60,982,218 bp (33.93%)
number of G's = 43,492,322 bp (24.2%)
number of N's = 11,994 bp (0.01%)
GC percentage = 41.6%
>>>>>>> Mismatches and indels
general error rate = 0.0064
number of mismatches = 1,129,548
number of insertions = 11,729
mapped reads with insertion percentage = 0.4%
number of deletions = 52,653
mapped reads with deletion percentage = 1.78%
homopolymer indels = 40.58%
>>>>>>> Coverage
mean coverageData = 0.0581X
std coverageData = 0.9722X
There is a 2.52% of reference with a coverageData >= 1X
There is a 1.22% of reference with a coverageData >= 2X
There is a 0.72% of reference with a coverageData >= 3X
There is a 0.44% of reference with a coverageData >= 4X
There is a 0.28% of reference with a coverageData >= 5X
There is a 0.18% of reference with a coverageData >= 6X
There is a 0.11% of reference with a coverageData >= 7X
There is a 0.07% of reference with a coverageData >= 8X
There is a 0.05% of reference with a coverageData >= 9X
There is a 0.03% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.02% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% 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 21171196 0.08493939118410461 1.0298488780012052
chr2 243199373 8092669 0.033275862927492 2.2802937307827156
chr3 198022430 17286498 0.08729565635569668 0.6054195788766679
chr4 191154276 10770776 0.05634598516645267 0.47541749202230177
chr5 180915260 7905980 0.04369990679614312 0.4232681633125973
chr6 171115067 3908482 0.022841249859078747 0.7033009086616498
chr7 159138663 10722196 0.06737643635978015 1.2512680643562386
chr8 146364022 10691615 0.07304810877634943 1.1243214204285608
chr9 141213431 6064440 0.04294520681959778 0.6068569978804405
chr10 135534747 12153040 0.08966733822139351 0.6704525120089707
chr11 135006516 2752712 0.020389475127259783 0.3694716140885376
chr12 133851895 1612702 0.012048406188048364 0.24537140000686317
chr13 115169878 1726962 0.014994910387940152 0.44284202519734805
chr14 107349540 6379323 0.059425713421780844 0.5170939614147056
chr15 102531392 2526424 0.024640492543005755 0.48342223476588647
chr16 90354753 4350646 0.04815071543607673 0.5094730455701914
chr17 81195210 6647486 0.08187042068121998 0.6135679365834202
chr18 78077248 23468104 0.30057545061014446 2.07598136265574
chr19 59128983 3190037 0.05395047975034511 0.7321935431725998
chr20 63025520 4741411 0.07523001793559181 0.5767776113037891
chr21 48129895 4816986 0.10008303570992623 0.6560635339242823
chr22 51304566 1494125 0.029122651578418965 0.34640162656452395
chrMT 16571 111206 6.710880453804839 6.364884515552034
chrX 155270560 6744383 0.043436328174510354 0.4472357260796014
chrY 59373566 467154 0.007868046867860353 0.3153271578825205