BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524512.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 = 3,984,429
number of mapped reads = 3,640,728 (91.37%)
number of supplementary alignments = 16,487 (0.41%)
number of secondary alignments = 0
number of mapped bases = 211,946,516 bp
number of sequenced bases = 211,881,785 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 447,738
duplication rate = 8.8%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.7922
>>>>>>> ACTG content
number of A's = 50,517,323 bp (23.84%)
number of C's = 37,997,738 bp (17.93%)
number of T's = 69,760,727 bp (32.92%)
number of G's = 53,602,880 bp (25.3%)
number of N's = 3,117 bp (0%)
GC percentage = 43.23%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 1,084,420
number of insertions = 14,923
mapped reads with insertion percentage = 0.41%
number of deletions = 38,149
mapped reads with deletion percentage = 1.04%
homopolymer indels = 43.63%
>>>>>>> Coverage
mean coverageData = 0.0685X
std coverageData = 0.6083X
There is a 4.83% of reference with a coverageData >= 1X
There is a 1.25% of reference with a coverageData >= 2X
There is a 0.39% of reference with a coverageData >= 3X
There is a 0.14% of reference with a coverageData >= 4X
There is a 0.05% of reference with a coverageData >= 5X
There is a 0.03% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% 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 21044040 0.08442923799174808 1.2137112290784902
chr2 243199373 16304987 0.06704370491942016 0.7853754968545471
chr3 198022430 11107161 0.05609041864600894 0.32095083202211366
chr4 191154276 12387953 0.06480604702768983 0.48237951578013816
chr5 180915260 11553327 0.0638604338849028 0.3438162233967257
chr6 171115067 9029885 0.05277083519477569 0.4072437160136272
chr7 159138663 9298017 0.058427140361233275 0.5600045685567087
chr8 146364022 19869441 0.1357535870393067 0.6802841747483125
chr9 141213431 9100568 0.06444548465081909 0.4669377113715171
chr10 135534747 11184706 0.08252279395187125 0.6922068614863691
chr11 135006516 6835997 0.05063457085286165 0.49176142178184
chr12 133851895 9939201 0.07425521319664544 0.37259566302682734
chr13 115169878 4554741 0.03954802313848071 0.27185980456805664
chr14 107349540 5266625 0.049060526947763354 0.3074531517250456
chr15 102531392 5791025 0.056480506965125375 0.3240514765848352
chr16 90354753 6690268 0.07404445010214349 0.4075412704560859
chr17 81195210 7316117 0.09010527837787476 0.44477311764101646
chr18 78077248 5094569 0.0652503658940438 0.9857554523009137
chr19 59128983 4533412 0.07666987947348934 0.8258003936703252
chr20 63025520 6125390 0.09718904342241048 0.4419957971569336
chr21 48129895 2980386 0.061923800166196086 0.4484079547383781
chr22 51304566 1784435 0.0347812122609126 0.25651965312217007
chrMT 16571 29310 1.7687526401544869 1.9858955564697915
chrX 155270560 13256270 0.08537529587064026 0.44526538900729157
chrY 59373566 868685 0.014630837568354914 0.49530840768035334