BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716228.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 = 1,703,674
number of mapped reads = 1,535,019 (90.1%)
number of supplementary alignments = 5,371 (0.32%)
number of secondary alignments = 0
number of mapped bases = 87,435,487 bp
number of sequenced bases = 87,410,733 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 57,071
duplication rate = 2.8%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.0933
>>>>>>> ACTG content
number of A's = 22,355,825 bp (25.58%)
number of C's = 16,835,734 bp (19.26%)
number of T's = 27,461,012 bp (31.42%)
number of G's = 20,756,858 bp (23.75%)
number of N's = 1,304 bp (0%)
GC percentage = 43.01%
>>>>>>> Mismatches and indels
general error rate = 0.0056
number of mismatches = 484,876
number of insertions = 4,848
mapped reads with insertion percentage = 0.31%
number of deletions = 14,941
mapped reads with deletion percentage = 0.97%
homopolymer indels = 44.43%
>>>>>>> Coverage
mean coverageData = 0.0282X
std coverageData = 0.2611X
There is a 2.54% of reference with a coverageData >= 1X
There is a 0.2% of reference with a coverageData >= 2X
There is a 0.03% 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 7158009 0.02871811902125612 0.42781244838585336
chr2 243199373 7527337 0.03095130101342819 0.2923880905053489
chr3 198022430 5910610 0.029848184369821135 0.18738852188751234
chr4 191154276 5936678 0.03105699817042021 0.2101922178453536
chr5 180915260 3475084 0.019208352020719535 0.15268152907275
chr6 171115067 5219378 0.030502153267426765 0.20860907431631515
chr7 159138663 4917055 0.030897928305455225 0.31725982278439724
chr8 146364022 4553446 0.031110418651928 0.2724631472740389
chr9 141213431 3776933 0.026746273164342277 0.27095856145776737
chr10 135534747 4311854 0.03181364259306877 0.26792491362319815
chr11 135006516 3907608 0.028943847421408906 0.252492172444116
chr12 133851895 4009046 0.02995135780483347 0.195410007198675
chr13 115169878 2782592 0.024160761896439623 0.1677494528429111
chr14 107349540 2712455 0.025267504639516852 0.18771365513301258
chr15 102531392 2528709 0.02466277840058974 0.17098829056649412
chr16 90354753 2623231 0.02903257341647539 0.2007695012577444
chr17 81195210 2368599 0.029171659264136396 0.20317788046231383
chr18 78077248 2339670 0.029966092042588387 0.4788730908897479
chr19 59128983 1802996 0.030492592778062832 0.345656180442501
chr20 63025520 1884740 0.02990439428345851 0.19428079253760258
chr21 48129895 1188145 0.024686216331866087 0.1943989742416883
chr22 51304566 1023377 0.019947093987696923 0.15239455866361012
chrMT 16571 1376 0.08303663025767907 0.2949642320375265
chrX 155270560 5219070 0.03361274667908714 0.2351380914258033
chrY 59373566 257489 0.004336761581744981 0.11419017619462275