BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525227.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 = 492,072
number of mapped reads = 460,893 (93.66%)
number of supplementary alignments = 1,912 (0.39%)
number of secondary alignments = 0
number of mapped bases = 29,036,319 bp
number of sequenced bases = 29,026,047 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 7,218
duplication rate = 1.14%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.7705
>>>>>>> ACTG content
number of A's = 8,066,009 bp (27.79%)
number of C's = 5,901,622 bp (20.33%)
number of T's = 8,699,372 bp (29.97%)
number of G's = 6,358,321 bp (21.91%)
number of N's = 723 bp (0%)
GC percentage = 42.24%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 140,250
number of insertions = 2,246
mapped reads with insertion percentage = 0.48%
number of deletions = 6,226
mapped reads with deletion percentage = 1.34%
homopolymer indels = 41.77%
>>>>>>> Coverage
mean coverageData = 0.0094X
std coverageData = 0.1225X
There is a 0.89% of reference with a coverageData >= 1X
There is a 0.03% of reference with a coverageData >= 2X
There is a 0% 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 2351469 0.009434155030650856 0.1986596691050584
chr2 243199373 2456600 0.01010117735788735 0.12372066857072526
chr3 198022430 1907290 0.009631686673070319 0.10170992061966036
chr4 191154276 1830227 0.009574606638671268 0.10578010493314878
chr5 180915260 1765246 0.009757308476907919 0.1019879179684813
chr6 171115067 1651918 0.009653843048198671 0.10599435673336716
chr7 159138663 1622208 0.01019367619043023 0.15584518760611052
chr8 146364022 1469132 0.010037521379400192 0.11323595209346404
chr9 141213431 1214644 0.008601476441713253 0.11079187628880398
chr10 135534747 1411738 0.01041605958064761 0.1338886277614571
chr11 135006516 1320448 0.009780624218167366 0.109085352626191
chr12 133851895 1300874 0.009718756689996806 0.10200724121072445
chr13 115169878 916329 0.007956325177317631 0.09149749621735513
chr14 107349540 879402 0.008191949401925708 0.09381353551647928
chr15 102531392 821996 0.008017017851469334 0.09196426738560994
chr16 90354753 852604 0.00943618317455862 0.10723657279167767
chr17 81195210 784697 0.009664326257669633 0.10438828538456589
chr18 78077248 780793 0.010000262816640258 0.17110460931643898
chr19 59128983 599846 0.010144703486613324 0.15623218748525466
chr20 63025520 625365 0.009922409208206454 0.10351110796619935
chr21 48129895 389192 0.008086284002905056 0.09926500701098889
chr22 51304566 348180 0.0067865304620255435 0.08483314593554633
chrMT 16571 14579 0.879789994568825 0.9923009521916758
chrX 155270560 1628279 0.01048672072799892 0.10775374382480069
chrY 59373566 93263 0.00157078320005236 0.06354543494073531