BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524854.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 = 1,372,279
number of mapped reads = 1,257,685 (91.65%)
number of supplementary alignments = 6,506 (0.47%)
number of secondary alignments = 0
number of mapped bases = 73,287,828 bp
number of sequenced bases = 73,266,764 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 34,332
duplication rate = 1.85%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.8491
>>>>>>> ACTG content
number of A's = 19,237,992 bp (26.26%)
number of C's = 13,951,939 bp (19.04%)
number of T's = 23,169,266 bp (31.62%)
number of G's = 16,897,838 bp (23.06%)
number of N's = 9,729 bp (0.01%)
GC percentage = 42.11%
>>>>>>> Mismatches and indels
general error rate = 0.0049
number of mismatches = 352,859
number of insertions = 4,291
mapped reads with insertion percentage = 0.34%
number of deletions = 13,479
mapped reads with deletion percentage = 1.06%
homopolymer indels = 45.13%
>>>>>>> Coverage
mean coverageData = 0.0237X
std coverageData = 0.248X
There is a 2.18% of reference with a coverageData >= 1X
There is a 0.13% 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 6077735 0.02438403152463961 0.47892699034367037
chr2 243199373 4772218 0.019622657497558597 0.24733418920174818
chr3 198022430 5294828 0.02673852653964503 0.1730674112765793
chr4 191154276 3955404 0.02069220779555044 0.16329864208004977
chr5 180915260 4401672 0.02433002058532818 0.16533543722362382
chr6 171115067 4763356 0.027837151242795 0.1906024703435107
chr7 159138663 3352700 0.02106779042123786 0.33658162439605865
chr8 146364022 7964681 0.054416931778494035 0.3373839625105844
chr9 141213431 3016760 0.0213631237385628 0.2063451276324342
chr10 135534747 3632157 0.026798714576122682 0.22488659866681507
chr11 135006516 3536133 0.026192313562109847 0.21976728274237217
chr12 133851895 2912684 0.021760498796076066 0.15952630436147672
chr13 115169878 1939983 0.01684453464472716 0.13680394959166542
chr14 107349540 1522809 0.014185519565337682 0.13475151735804583
chr15 102531392 2195288 0.021410886531219628 0.15682094889983403
chr16 90354753 2109437 0.023346165309090047 0.17353713847506808
chr17 81195210 2015067 0.024817560050648307 0.1848548172221918
chr18 78077248 1764442 0.022598670485926963 0.37188221681489
chr19 59128983 1066476 0.018036434010711803 0.32040268291354584
chr20 63025520 1562000 0.02478361146405456 0.16793521978927797
chr21 48129895 1057646 0.02197482458667321 0.1658166675204144
chr22 51304566 438289 0.008542884857460836 0.09713399113791128
chrMT 16571 9119 0.5502987146219299 0.8281499105732412
chrX 155270560 3746884 0.024131322769751072 0.18560063264206839
chrY 59373566 180060 0.003032662717277248 0.08736299872811261