BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524872.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 = 1,688,799
number of mapped reads = 1,563,251 (92.57%)
number of supplementary alignments = 7,870 (0.47%)
number of secondary alignments = 0
number of mapped bases = 91,784,593 bp
number of sequenced bases = 91,757,671 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 48,376
duplication rate = 2.09%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.5251
>>>>>>> ACTG content
number of A's = 23,617,636 bp (25.74%)
number of C's = 17,472,684 bp (19.04%)
number of T's = 29,081,720 bp (31.69%)
number of G's = 21,573,810 bp (23.51%)
number of N's = 11,821 bp (0.01%)
GC percentage = 42.55%
>>>>>>> Mismatches and indels
general error rate = 0.0049
number of mismatches = 437,363
number of insertions = 6,117
mapped reads with insertion percentage = 0.39%
number of deletions = 17,143
mapped reads with deletion percentage = 1.09%
homopolymer indels = 42.88%
>>>>>>> Coverage
mean coverageData = 0.0296X
std coverageData = 0.3001X
There is a 2.7% of reference with a coverageData >= 1X
There is a 0.18% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 7805038 0.03131401626477793 0.608526644304791
chr2 243199373 6092289 0.02505059501119684 0.2800710340807269
chr3 198022430 6764767 0.03416161997406052 0.1967649790586381
chr4 191154276 5121381 0.026791872550107117 0.18651515019816295
chr5 180915260 5292562 0.02925437025046975 0.18420930674711522
chr6 171115067 6092732 0.03560605215436698 0.22158760676152298
chr7 159138663 4262966 0.026787745477037217 0.4049106388806627
chr8 146364022 10154628 0.06937926316345693 0.4191090419601595
chr9 141213431 3840133 0.027193822661245304 0.25220029756911877
chr10 135534747 3625772 0.02675160488549848 0.2567311057405112
chr11 135006516 4483818 0.03321186364071494 0.26678734958293776
chr12 133851895 3686847 0.0275442271474752 0.18309141464668738
chr13 115169878 2479116 0.021525732622552574 0.15670176615465667
chr14 107349540 1964585 0.018300823645820932 0.1559586192174344
chr15 102531392 2757892 0.026898025533487344 0.1756356985650038
chr16 90354753 2624074 0.029041903307510563 0.19588966726841162
chr17 81195210 2534912 0.031219969749447043 0.21367065120314935
chr18 78077248 2275527 0.029144559500867653 0.47530868815621735
chr19 59128983 1321186 0.022344135362517566 0.3888578581478629
chr20 63025520 1960404 0.031104923846721137 0.19050071481752545
chr21 48129895 1253997 0.0260544304117015 0.18498388005586805
chr22 51304566 533257 0.010393948172176332 0.1069476946456934
chrMT 16571 9821 0.5926618791865307 0.8825297219166761
chrX 155270560 4618144 0.029742560341123263 0.21106675172273026
chrY 59373566 228745 0.00385264041577021 0.10375015736756038