BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524374.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 = 1,146,510
number of mapped reads = 1,046,997 (91.32%)
number of supplementary alignments = 3,904 (0.34%)
number of secondary alignments = 0
number of mapped bases = 61,379,915 bp
number of sequenced bases = 61,362,437 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 28,548
duplication rate = 1.97%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.74
>>>>>>> ACTG content
number of A's = 15,888,955 bp (25.89%)
number of C's = 11,440,068 bp (18.64%)
number of T's = 19,613,532 bp (31.96%)
number of G's = 14,411,900 bp (23.49%)
number of N's = 7,982 bp (0.01%)
GC percentage = 42.13%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 295,407
number of insertions = 4,847
mapped reads with insertion percentage = 0.46%
number of deletions = 10,963
mapped reads with deletion percentage = 1.04%
homopolymer indels = 43.03%
>>>>>>> Coverage
mean coverageData = 0.0198X
std coverageData = 0.2162X
There is a 1.84% of reference with a coverageData >= 1X
There is a 0.1% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% 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 5207286 0.020891767407070973 0.43353826103330634
chr2 243199373 5069266 0.020844075120210116 0.23143867988869427
chr3 198022430 4348871 0.021961507087858684 0.15619175813596667
chr4 191154276 4136385 0.021638987557882305 0.1655036115120052
chr5 180915260 3889523 0.021499142747825696 0.1540962499477988
chr6 171115067 2394616 0.013994185561695745 0.13416022759569604
chr7 159138663 3431401 0.0215623339753709 0.2991075002841949
chr8 146364022 3224981 0.022033973622288133 0.20273861094683276
chr9 141213431 2160662 0.015300683403124736 0.15776100637666976
chr10 135534747 3064471 0.022610224077815263 0.2034061460584713
chr11 135006516 2568426 0.019024459530531106 0.17389113601715134
chr12 133851895 2793204 0.020867870417523787 0.1543123249107666
chr13 115169878 1981171 0.017202162878040037 0.13767254084682004
chr14 107349540 1733014 0.016143655575981044 0.1377829084330474
chr15 102531392 1820332 0.017753899215569025 0.14054193143609336
chr16 90354753 1791281 0.019824978106021716 0.15530017681023364
chr17 81195210 1615323 0.01989431396260937 0.15989447305976948
chr18 78077248 1682326 0.02154694284306742 0.26197686120280833
chr19 59128983 1670612 0.028253690749255742 0.32322423313239246
chr20 63025520 1721217 0.027309842108403072 0.1779734563087944
chr21 48129895 824154 0.01712353621382303 0.14701412254595878
chr22 51304566 431402 0.008408647292718547 0.09663447962213807
chrMT 16571 9830 0.5932049966809486 0.8836342793913915
chrX 155270560 3625193 0.023347587591620717 0.17265750560820406
chrY 59373566 184968 0.0031153257663519823 0.08889399900030473