BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524404.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 = 1,164,540
number of mapped reads = 1,081,901 (92.9%)
number of supplementary alignments = 4,095 (0.35%)
number of secondary alignments = 0
number of mapped bases = 63,604,153 bp
number of sequenced bases = 63,585,943 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 31,830
duplication rate = 2.2%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.7745
>>>>>>> ACTG content
number of A's = 15,915,213 bp (25.03%)
number of C's = 11,955,654 bp (18.8%)
number of T's = 20,238,501 bp (31.83%)
number of G's = 15,467,775 bp (24.33%)
number of N's = 8,800 bp (0.01%)
GC percentage = 43.13%
>>>>>>> Mismatches and indels
general error rate = 0.0049
number of mismatches = 303,843
number of insertions = 4,348
mapped reads with insertion percentage = 0.4%
number of deletions = 11,533
mapped reads with deletion percentage = 1.06%
homopolymer indels = 43.79%
>>>>>>> Coverage
mean coverageData = 0.0205X
std coverageData = 0.2161X
There is a 1.89% of reference with a coverageData >= 1X
There is a 0.12% 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 5305944 0.021287585879274498 0.42263886505106557
chr2 243199373 5270224 0.021670384816329276 0.2388866439070853
chr3 198022430 4398043 0.02220982239234212 0.15813655170339755
chr4 191154276 4274457 0.022361294183134046 0.17215921304650092
chr5 180915260 3901104 0.021563156142826206 0.15584932627469744
chr6 171115067 2538551 0.014835344686508524 0.13714150300217967
chr7 159138663 3601967 0.022634141396550504 0.295660572189941
chr8 146364022 3298999 0.02253968533332597 0.2016581060095055
chr9 141213431 2399519 0.016992144323722296 0.16935940289099158
chr10 135534747 3192185 0.02355252118484421 0.202007959352943
chr11 135006516 2601653 0.01927057357735237 0.17560094151397346
chr12 133851895 2925659 0.021857434293328457 0.15923947144830924
chr13 115169878 2069494 0.017969056110313845 0.142592973127557
chr14 107349540 1710453 0.015933491657253492 0.13691934950224996
chr15 102531392 1983197 0.019342339563672362 0.14760628598752348
chr16 90354753 1964496 0.021742032762792234 0.16091389571536477
chr17 81195210 1670306 0.02057148445086847 0.16408056061923876
chr18 78077248 1768513 0.022650811155639092 0.2643616237068085
chr19 59128983 1750316 0.029601659138970816 0.28997128216934825
chr20 63025520 1733449 0.027503922220713132 0.1793841732855127
chr21 48129895 859372 0.01785526438401746 0.1536085890468
chr22 51304566 435297 0.00848456646139449 0.09695133085036173
chrMT 16571 45442 2.742260575704544 2.196472085391755
chrX 155270560 3711439 0.023903043822344688 0.17830949005615307
chrY 59373566 194074 0.0032686936809555958 0.09388173336813661