BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524998.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 = 1,799,272
number of mapped reads = 1,666,530 (92.62%)
number of supplementary alignments = 5,420 (0.3%)
number of secondary alignments = 0
number of mapped bases = 97,189,165 bp
number of sequenced bases = 97,158,681 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 72,562
duplication rate = 3.32%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.3713
>>>>>>> ACTG content
number of A's = 23,740,309 bp (24.43%)
number of C's = 19,085,387 bp (19.64%)
number of T's = 30,297,263 bp (31.18%)
number of G's = 24,034,748 bp (24.74%)
number of N's = 974 bp (0%)
GC percentage = 44.38%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 471,535
number of insertions = 6,132
mapped reads with insertion percentage = 0.37%
number of deletions = 18,545
mapped reads with deletion percentage = 1.11%
homopolymer indels = 44.49%
>>>>>>> Coverage
mean coverageData = 0.0314X
std coverageData = 0.293X
There is a 2.79% of reference with a coverageData >= 1X
There is a 0.25% of reference with a coverageData >= 2X
There is a 0.04% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% 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 11073582 0.044427500142517194 0.6123684101531188
chr2 243199373 8403946 0.0345557881022991 0.31901929102165993
chr3 198022430 5548434 0.028019219842923854 0.18297219464910727
chr4 191154276 6442749 0.033704446140665985 0.23044677202500977
chr5 180915260 4405243 0.02434975910821453 0.1737848155492656
chr6 171115067 5914783 0.03456611450819816 0.2678074026975536
chr7 159138663 6441943 0.04048006234663414 0.3687313519419201
chr8 146364022 5989553 0.0409223039798674 0.3002949896498321
chr9 141213431 2850171 0.020183427169898592 0.1978834430878519
chr10 135534747 5326679 0.0393012059114258 0.2964606450704944
chr11 135006516 4338340 0.03213430083626482 0.24116431019578044
chr12 133851895 4337880 0.032408058175044885 0.20029762932131287
chr13 115169878 1953432 0.016961309970303172 0.14606017554319112
chr14 107349540 2313990 0.021555658272965118 0.1638653893764287
chr15 102531392 2120249 0.020679022869405695 0.1619088841312822
chr16 90354753 3401895 0.03765042664662035 0.22128605761896175
chr17 81195210 2667449 0.03285229510460038 0.2615654885015886
chr18 78077248 1325806 0.016980695836000776 0.3068804139885655
chr19 59128983 2666047 0.04508866658504849 0.3595310735563633
chr20 63025520 2420657 0.03840756887051468 0.21768043827423755
chr21 48129895 1509362 0.03136017645581816 0.21011064676778454
chr22 51304566 1156405 0.022540001605315208 0.1634854115930375
chrMT 16571 64355 3.883591817029751 2.9647977652791226
chrX 155270560 4236811 0.027286634375505568 0.2010796693123976
chrY 59373566 279404 0.004705865233023059 0.13692752916478404