BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9867838.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 = 34,652,781
number of mapped reads = 31,316,914 (90.37%)
number of supplementary alignments = 85,182 (0.25%)
number of secondary alignments = 0
number of mapped bases = 2,794,599,797 bp
number of sequenced bases = 2,793,868,050 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,864,211
duplication rate = 1.59%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 50.3853
>>>>>>> ACTG content
number of A's = 785,744,415 bp (28.12%)
number of C's = 605,662,030 bp (21.68%)
number of T's = 784,412,887 bp (28.08%)
number of G's = 613,901,332 bp (21.97%)
number of N's = 4,147,386 bp (0.15%)
GC percentage = 43.65%
>>>>>>> Mismatches and indels
general error rate = 0.0049
number of mismatches = 12,843,905
number of insertions = 287,614
mapped reads with insertion percentage = 0.9%
number of deletions = 288,545
mapped reads with deletion percentage = 0.9%
homopolymer indels = 35.92%
>>>>>>> Coverage
mean coverageData = 0.9027X
std coverageData = 10.4684X
There is a 52.21% of reference with a coverageData >= 1X
There is a 21.77% of reference with a coverageData >= 2X
There is a 7.71% of reference with a coverageData >= 3X
There is a 2.56% of reference with a coverageData >= 4X
There is a 0.87% of reference with a coverageData >= 5X
There is a 0.33% of reference with a coverageData >= 6X
There is a 0.16% of reference with a coverageData >= 7X
There is a 0.09% of reference with a coverageData >= 8X
There is a 0.07% of reference with a coverageData >= 9X
There is a 0.05% of reference with a coverageData >= 10X
There is a 0.05% of reference with a coverageData >= 11X
There is a 0.04% of reference with a coverageData >= 12X
There is a 0.04% of reference with a coverageData >= 13X
There is a 0.03% of reference with a coverageData >= 14X
There is a 0.03% of reference with a coverageData >= 15X
There is a 0.03% of reference with a coverageData >= 16X
There is a 0.03% of reference with a coverageData >= 17X
There is a 0.03% of reference with a coverageData >= 18X
There is a 0.02% of reference with a coverageData >= 19X
There is a 0.02% of reference with a coverageData >= 20X
There is a 0.02% of reference with a coverageData >= 21X
There is a 0.02% of reference with a coverageData >= 22X
There is a 0.02% of reference with a coverageData >= 23X
There is a 0.02% of reference with a coverageData >= 24X
There is a 0.02% of reference with a coverageData >= 25X
There is a 0.02% of reference with a coverageData >= 26X
There is a 0.02% of reference with a coverageData >= 27X
There is a 0.02% of reference with a coverageData >= 28X
There is a 0.02% of reference with a coverageData >= 29X
There is a 0.02% of reference with a coverageData >= 30X
There is a 0.02% of reference with a coverageData >= 31X
There is a 0.02% of reference with a coverageData >= 32X
There is a 0.02% of reference with a coverageData >= 33X
There is a 0.02% of reference with a coverageData >= 34X
There is a 0.02% of reference with a coverageData >= 35X
There is a 0.02% of reference with a coverageData >= 36X
There is a 0.02% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% of reference with a coverageData >= 40X
There is a 0.01% of reference with a coverageData >= 41X
There is a 0.01% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 265081346 1.063513282079245 21.485702893737248
chr2 243199373 220970026 0.9085961993824713 6.604630828077636
chr3 198022430 155042541 0.7829544410701353 5.408853659637866
chr4 191154276 160321873 0.8387040894654118 7.939154899296224
chr5 180915260 150312853 0.830846734543012 1.2725420909704324
chr6 171115067 125852042 0.7354819432703725 4.461105713573096
chr7 159138663 139087198 0.874000041083668 8.620450285082024
chr8 146364022 215545282 1.4726657484173262 4.245119909649524
chr9 141213431 117376748 0.831201020815081 7.830031087319203
chr10 135534747 164199714 1.2114953370592119 30.252538676990735
chr11 135006516 104842425 0.7765730729619006 3.82300533097096
chr12 133851895 124073285 0.9269445531570547 1.9292651004294912
chr13 115169878 65913337 0.5723140298889611 0.8925524572733035
chr14 107349540 68682691 0.639804241359581 1.2703729416923966
chr15 102531392 74223396 0.7239089858450376 1.0070201356454245
chr16 90354753 100504617 1.1123334817815285 8.997703954344248
chr17 81195210 100297474 1.2352634348750375 3.5749794664520453
chr18 78077248 67712767 0.8672535051440338 11.094728890190368
chr19 59128983 63447252 1.073031342345259 13.455951065381418
chr20 63025520 77772305 1.2339811714365863 2.582271324488067
chr21 48129895 39445800 0.8195696250739795 5.665821781101357
chr22 51304566 29702951 0.578953362552565 1.1250712972689754
chrMT 16571 4692647 283.1842978697725 86.18535621915798
chrX 155270560 144956171 0.9335715089840598 2.6328802427782976
chrY 59373566 14543056 0.24494159572628668 12.073544612643136