BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716864.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 = 1,636,794
number of mapped reads = 1,515,676 (92.6%)
number of supplementary alignments = 29,074 (1.78%)
number of secondary alignments = 0
number of mapped bases = 115,262,482 bp
number of sequenced bases = 115,219,072 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 70,033
duplication rate = 3.66%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.4246
>>>>>>> ACTG content
number of A's = 29,369,380 bp (25.49%)
number of C's = 23,267,005 bp (20.19%)
number of T's = 34,726,999 bp (30.14%)
number of G's = 27,851,220 bp (24.17%)
number of N's = 4,468 bp (0%)
GC percentage = 44.37%
>>>>>>> Mismatches and indels
general error rate = 0.0067
number of mismatches = 746,409
number of insertions = 8,985
mapped reads with insertion percentage = 0.58%
number of deletions = 21,599
mapped reads with deletion percentage = 1.4%
homopolymer indels = 39.2%
>>>>>>> Coverage
mean coverageData = 0.0372X
std coverageData = 0.3208X
There is a 3.14% of reference with a coverageData >= 1X
There is a 0.41% of reference with a coverageData >= 2X
There is a 0.08% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% 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 12707631 0.05098334739956375 0.6236956056095895
chr2 243199373 10875378 0.04471795245952381 0.3389498725402815
chr3 198022430 7457878 0.0376617840716327 0.2240636987446556
chr4 191154276 5575459 0.029167325558545183 0.2589453734459955
chr5 180915260 6984797 0.03860811409717456 0.23024525137068025
chr6 171115067 7102264 0.0415057780972613 0.24497121545516146
chr7 159138663 7213734 0.04532986430833593 0.4094667817582853
chr8 146364022 7170160 0.04898854173329563 0.3444219652055918
chr9 141213431 3493801 0.024741279744134252 0.22637296386034733
chr10 135534747 6083979 0.044888702968545774 0.39760588829218885
chr11 135006516 3410043 0.025258358641000705 0.24960341605850908
chr12 133851895 4046987 0.030234812887781678 0.1993150099209015
chr13 115169878 2203466 0.019132311662255992 0.1557892918945144
chr14 107349540 2215312 0.020636436821247675 0.1773609488709506
chr15 102531392 2347234 0.02289283266533629 0.173232638516413
chr16 90354753 3428587 0.0379458399936083 0.23652171000710087
chr17 81195210 2082385 0.02564664836755764 0.20487910924565922
chr18 78077248 3416656 0.04375994399802616 0.339760874870112
chr19 59128983 2757826 0.046640849547505324 0.4534282510786175
chr20 63025520 3088674 0.049006719817623084 0.26865756221177806
chr21 48129895 2004988 0.04165785111311795 0.26575401966580975
chr22 51304566 1721776 0.033559897963077984 0.21411134671165485
chrMT 16571 111650 6.737674250196126 5.554594612348577
chrX 155270560 7400002 0.04765875771942859 0.265934681549423
chrY 59373566 361815 0.006093873492456222 0.21966898929459902