BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524865.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,129,002
number of mapped reads = 1,030,758 (91.3%)
number of supplementary alignments = 5,704 (0.51%)
number of secondary alignments = 0
number of mapped bases = 59,925,804 bp
number of sequenced bases = 59,907,762 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 24,720
duplication rate = 1.62%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9576
>>>>>>> ACTG content
number of A's = 16,244,131 bp (27.12%)
number of C's = 10,866,962 bp (18.14%)
number of T's = 18,503,208 bp (30.89%)
number of G's = 14,285,483 bp (23.85%)
number of N's = 7,978 bp (0.01%)
GC percentage = 41.99%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 292,323
number of insertions = 4,962
mapped reads with insertion percentage = 0.48%
number of deletions = 11,589
mapped reads with deletion percentage = 1.12%
homopolymer indels = 43.47%
>>>>>>> Coverage
mean coverageData = 0.0194X
std coverageData = 0.2102X
There is a 1.81% of reference with a coverageData >= 1X
There is a 0.08% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% 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 5041571 0.020226914499843915 0.39640815266662
chr2 243199373 3907656 0.016067705898238478 0.20747777444498788
chr3 198022430 4420897 0.0223252335606628 0.1558827487140956
chr4 191154276 3259113 0.017049647374877453 0.14254511312241727
chr5 180915260 3642031 0.02013114316614309 0.149065105384323
chr6 171115067 3901536 0.022800657291037967 0.17088211429301
chr7 159138663 2754879 0.017311186031517684 0.27129233177247597
chr8 146364022 6265626 0.04280851205359743 0.28576442598828505
chr9 141213431 2452849 0.01736979961913113 0.17888347855696413
chr10 135534747 3027168 0.022334995763116008 0.202036923372316
chr11 135006516 2887311 0.021386456635915263 0.18932892189087708
chr12 133851895 2359096 0.0176246738979676 0.1426667150889226
chr13 115169878 1600557 0.0138973577796097 0.12289032333225082
chr14 107349540 1300137 0.012111248916390326 0.12177199084381272
chr15 102531392 1790444 0.017462398247748357 0.13969082768757538
chr16 90354753 1715521 0.018986505336360114 0.1507990667478313
chr17 81195210 1568229 0.01931430437830015 0.15734212868972372
chr18 78077248 1446946 0.018532236177176736 0.30848320425176073
chr19 59128983 873482 0.01477248475591065 0.25719754830801805
chr20 63025520 1253906 0.019895210701950574 0.1489102403814809
chr21 48129895 873618 0.018151255056758384 0.1487176678970669
chr22 51304566 365665 0.007127338334759523 0.08756681438007252
chrMT 16571 2476 0.14941765735320742 0.3830991302520417
chrX 155270560 3063851 0.019732336896318273 0.1624965628086779
chrY 59373566 151239 0.002547244677875673 0.07475233944207431