BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716558.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 = 24,088,948
number of mapped reads = 23,549,671 (97.76%)
number of supplementary alignments = 12,231 (0.05%)
number of secondary alignments = 0
number of mapped bases = 1,598,013,844 bp
number of sequenced bases = 1,597,740,652 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,357,088
duplication rate = 1.87%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 49.0506
>>>>>>> ACTG content
number of A's = 454,525,386 bp (28.45%)
number of C's = 331,179,519 bp (20.73%)
number of T's = 475,377,381 bp (29.75%)
number of G's = 336,578,555 bp (21.07%)
number of N's = 79,811 bp (0%)
GC percentage = 41.79%
>>>>>>> Mismatches and indels
general error rate = 0.0032
number of mismatches = 4,812,683
number of insertions = 126,843
mapped reads with insertion percentage = 0.54%
number of deletions = 140,473
mapped reads with deletion percentage = 0.59%
homopolymer indels = 39.22%
>>>>>>> Coverage
mean coverageData = 0.5162X
std coverageData = 6.3968X
There is a 36.79% of reference with a coverageData >= 1X
There is a 9.63% of reference with a coverageData >= 2X
There is a 2.05% of reference with a coverageData >= 3X
There is a 0.44% of reference with a coverageData >= 4X
There is a 0.13% of reference with a coverageData >= 5X
There is a 0.06% of reference with a coverageData >= 6X
There is a 0.04% of reference with a coverageData >= 7X
There is a 0.03% of reference with a coverageData >= 8X
There is a 0.03% of reference with a coverageData >= 9X
There is a 0.03% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.02% of reference with a coverageData >= 12X
There is a 0.02% of reference with a coverageData >= 13X
There is a 0.02% of reference with a coverageData >= 14X
There is a 0.02% of reference with a coverageData >= 15X
There is a 0.02% of reference with a coverageData >= 16X
There is a 0.02% of reference with a coverageData >= 17X
There is a 0.02% of reference with a coverageData >= 18X
There is a 0.02% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% of reference with a coverageData >= 26X
There is a 0.01% of reference with a coverageData >= 27X
There is a 0.01% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% of reference with a coverageData >= 32X
There is a 0.01% of reference with a coverageData >= 33X
There is a 0.01% of reference with a coverageData >= 34X
There is a 0.01% of reference with a coverageData >= 35X
There is a 0.01% of reference with a coverageData >= 36X
There is a 0.01% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% of reference with a coverageData >= 40X
There is a 0.01% of reference with a coverageData >= 41X
There is a 0.01% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 161507603 0.6479727205975547 13.58493879221943
chr2 243199373 128888234 0.529969433761657 3.264739279713994
chr3 198022430 115018528 0.5808358578369127 3.246991813167485
chr4 191154276 86859554 0.45439503534830683 1.8635947038054093
chr5 180915260 75184931 0.4155809244615407 0.8700650101485248
chr6 171115067 91459346 0.534490314637226 2.1150600174748093
chr7 159138663 103876160 0.6527399315903515 7.068276794339728
chr8 146364022 83405528 0.5698499321096819 2.799040040622712
chr9 141213431 56645070 0.4011308952616554 2.575400391827238
chr10 135534747 97778711 0.721429103342776 18.69987330558963
chr11 135006516 72888661 0.5398899487192159 2.2921509204807835
chr12 133851895 69436913 0.5187592824143431 1.057689789013669
chr13 115169878 44801055 0.38899976085760896 0.7275127015700859
chr14 107349540 53921253 0.5022960787722053 1.2574430870129558
chr15 102531392 40915996 0.3990582318437655 0.7104893956941051
chr16 90354753 53975267 0.5973705334571608 5.662024777523303
chr17 81195210 37023296 0.45597881944021085 1.6312781362221587
chr18 78077248 35382385 0.45317151803301264 6.128677324181209
chr19 59128983 33648005 0.5690611150880103 9.799092073401274
chr20 63025520 31914906 0.5063806851573776 1.0903729444603762
chr21 48129895 21171203 0.4398763595889831 1.9261541112279355
chr22 51304566 18152042 0.3538094835457725 0.9613886424503619
chrMT 16571 6602490 398.43642507995895 85.74943467076929
chrX 155270560 72084854 0.46425319777297125 1.6142521119310895
chrY 59373566 5471853 0.09215975001400455 3.3060590959158893