BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716116.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 = 1,703,234
number of mapped reads = 1,286,378 (75.53%)
number of supplementary alignments = 4,692 (0.28%)
number of secondary alignments = 0
number of mapped bases = 71,540,136 bp
number of sequenced bases = 71,518,428 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 36,501
duplication rate = 1.85%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 41.852
>>>>>>> ACTG content
number of A's = 18,290,845 bp (25.58%)
number of C's = 13,535,703 bp (18.93%)
number of T's = 22,973,648 bp (32.12%)
number of G's = 16,717,191 bp (23.37%)
number of N's = 1,041 bp (0%)
GC percentage = 42.3%
>>>>>>> Mismatches and indels
general error rate = 0.0055
number of mismatches = 382,485
number of insertions = 5,221
mapped reads with insertion percentage = 0.4%
number of deletions = 13,755
mapped reads with deletion percentage = 1.06%
homopolymer indels = 38.79%
>>>>>>> Coverage
mean coverageData = 0.0231X
std coverageData = 0.251X
There is a 2.1% of reference with a coverageData >= 1X
There is a 0.14% 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 5797584 0.02326005839720656 0.28716913443036757
chr2 243199373 6984551 0.028719444930476856 0.3391688535862687
chr3 198022430 5478018 0.02766362376221724 0.1908219228533453
chr4 191154276 4089335 0.021392851290441443 0.16256597733509795
chr5 180915260 3584257 0.01981180028705152 0.15133221532267915
chr6 171115067 3978383 0.023249752752631653 0.18496283516225653
chr7 159138663 4504984 0.02830854498256027 0.6024220482384004
chr8 146364022 5306509 0.03625555602728654 0.2420958624020286
chr9 141213431 2912238 0.020622953350662516 0.17800328357651984
chr10 135534747 3357095 0.024769257141122637 0.31174517324286777
chr11 135006516 2115027 0.01566611051573244 0.16308540354843976
chr12 133851895 3334394 0.024911070553016824 0.1805383460854957
chr13 115169878 1911438 0.01659668337931208 0.13876968234625134
chr14 107349540 2294845 0.021377315636378135 0.15954450272425155
chr15 102531392 1666309 0.016251695870860703 0.1400525494390213
chr16 90354753 2131165 0.02358663965358856 0.17511284127138008
chr17 81195210 2883715 0.035515826610954024 0.20926614410202857
chr18 78077248 1674754 0.021449961965872566 0.266919142678111
chr19 59128983 1412814 0.023893764585803886 0.27588298113756565
chr20 63025520 1533325 0.024328637034648822 0.1703651768027438
chr21 48129895 731490 0.015198246329022742 0.13559939540982885
chr22 51304566 994814 0.019390359914554192 0.15071220861283094
chrMT 16571 59025 3.561945567557782 2.981034220651228
chrX 155270560 2637830 0.016988603634842305 0.16656630787888035
chrY 59373566 166237 0.002799848673397855 0.07521244321943672