BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716377.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 = 1,504,116
number of mapped reads = 1,319,031 (87.69%)
number of supplementary alignments = 5,086 (0.34%)
number of secondary alignments = 0
number of mapped bases = 74,793,639 bp
number of sequenced bases = 74,771,109 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 29,843
duplication rate = 1.57%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.0548
>>>>>>> ACTG content
number of A's = 18,894,943 bp (25.27%)
number of C's = 15,177,353 bp (20.3%)
number of T's = 22,823,858 bp (30.52%)
number of G's = 17,874,309 bp (23.91%)
number of N's = 646 bp (0%)
GC percentage = 44.2%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 389,042
number of insertions = 5,337
mapped reads with insertion percentage = 0.4%
number of deletions = 14,272
mapped reads with deletion percentage = 1.08%
homopolymer indels = 41.15%
>>>>>>> Coverage
mean coverageData = 0.0242X
std coverageData = 0.2133X
There is a 2.22% 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 6300117 0.0252762339155817 0.26528403645528037
chr2 243199373 5867290 0.02412543226416953 0.2880293125977651
chr3 198022430 4318976 0.02181053934142713 0.16252070181358141
chr4 191154276 4566852 0.023890922534215243 0.1793314117200473
chr5 180915260 4287946 0.023701405840502343 0.16357154754052713
chr6 171115067 4008986 0.023428597319253015 0.18958229966700157
chr7 159138663 4289118 0.026952080149121274 0.30301014336256377
chr8 146364022 3870314 0.02644306945869525 0.20609913808430388
chr9 141213431 2484888 0.017596683137031065 0.1619989822897677
chr10 135534747 3353452 0.024742378424921545 0.28081913860851637
chr11 135006516 2668149 0.019763112767090443 0.18288775992550343
chr12 133851895 3741404 0.027951819434457764 0.17995092567536627
chr13 115169878 2261883 0.019639536303060076 0.15057372695628055
chr14 107349540 2521504 0.023488726640095523 0.16901743629400526
chr15 102531392 2751793 0.02683854131230365 0.1793044081312605
chr16 90354753 2639694 0.02921477744507807 0.19620519760824426
chr17 81195210 3328832 0.04099788645167615 0.22734846438853668
chr18 78077248 1398715 0.0179145018021127 0.24674736732469715
chr19 59128983 1937778 0.03277205021435935 0.2710912288771147
chr20 63025520 2196323 0.03484815357334616 0.2083490110826506
chr21 48129895 945063 0.01963567549856487 0.160664117588792
chr22 51304566 715114 0.013938603437362671 0.1272064992134888
chrMT 16571 17867 1.078208919196186 1.1813750584251723
chrX 155270560 4086404 0.02631795750591741 0.18330404694628455
chrY 59373566 235177 0.003960971453188444 0.11935924629536265