BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524314.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 = 3,918,599
number of mapped reads = 3,566,937 (91.03%)
number of supplementary alignments = 15,103 (0.39%)
number of secondary alignments = 0
number of mapped bases = 207,642,888 bp
number of sequenced bases = 207,587,703 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 173,290
duplication rate = 3.35%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.7124
>>>>>>> ACTG content
number of A's = 50,949,399 bp (24.54%)
number of C's = 39,094,044 bp (18.83%)
number of T's = 66,503,623 bp (32.04%)
number of G's = 51,012,370 bp (24.57%)
number of N's = 28,267 bp (0.01%)
GC percentage = 43.41%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 1,067,001
number of insertions = 11,632
mapped reads with insertion percentage = 0.32%
number of deletions = 35,176
mapped reads with deletion percentage = 0.98%
homopolymer indels = 42.53%
>>>>>>> Coverage
mean coverageData = 0.0671X
std coverageData = 0.5731X
There is a 5.62% of reference with a coverageData >= 1X
There is a 0.74% of reference with a coverageData >= 2X
There is a 0.14% 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 17444142 0.06998635321353923 1.1854379267330712
chr2 243199373 13539081 0.05567070684840952 0.7626022173413266
chr3 198022430 14616527 0.07381248174764848 0.31990206143934935
chr4 191154276 10929378 0.057175691952609 0.32197038749604967
chr5 180915260 12330756 0.0681576335793896 0.3045811176735906
chr6 171115067 13445678 0.07857682105807784 0.3761276954004339
chr7 159138663 9547422 0.059994358504821675 0.7695885592566477
chr8 146364022 21752979 0.14862244630036198 0.6731981029184895
chr9 141213431 8586521 0.0608052714192604 0.41845845282120425
chr10 135534747 10444157 0.07705888881764025 0.5480161547298662
chr11 135006516 9936312 0.07359875874435572 0.45634930981100247
chr12 133851895 8297706 0.06199169612055175 0.2985892729968018
chr13 115169878 5405573 0.04693564926759756 0.2553086114467004
chr14 107349540 4405749 0.0410411539723412 0.2688857895788571
chr15 102531392 6263983 0.06109331861992082 0.30292343876512523
chr16 90354753 6373063 0.07053378807864152 0.34607169893450007
chr17 81195210 6219146 0.07659498632985862 0.38503199910805147
chr18 78077248 4900422 0.0627637644195656 0.8402622429448651
chr19 59128983 3551616 0.06006556885986015 0.7828236325639579
chr20 63025520 4625133 0.07338508274108647 0.329925999216126
chr21 48129895 2894183 0.060132751172633975 0.32116584313709484
chr22 51304566 1438066 0.02802998080131893 0.19343169896456763
chrMT 16571 11200 0.6758795486090158 0.9675347007629184
chrX 155270560 10133286 0.0652621205204644 0.3650045841544061
chrY 59373566 550809 0.009277007212266819 0.22999628607517908