BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716502.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 = 1,167,196
number of mapped reads = 1,075,140 (92.11%)
number of supplementary alignments = 3,658 (0.31%)
number of secondary alignments = 0
number of mapped bases = 62,213,265 bp
number of sequenced bases = 62,193,469 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 32,016
duplication rate = 2.1%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.4267
>>>>>>> ACTG content
number of A's = 15,765,465 bp (25.35%)
number of C's = 12,025,862 bp (19.34%)
number of T's = 19,682,721 bp (31.65%)
number of G's = 14,718,250 bp (23.67%)
number of N's = 1,171 bp (0%)
GC percentage = 43%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 314,667
number of insertions = 4,355
mapped reads with insertion percentage = 0.4%
number of deletions = 12,382
mapped reads with deletion percentage = 1.14%
homopolymer indels = 42.71%
>>>>>>> Coverage
mean coverageData = 0.0201X
std coverageData = 0.2075X
There is a 1.86% 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 5195993 0.020846459596182913 0.3130253092595378
chr2 243199373 4921137 0.02023499049070328 0.2751732251561064
chr3 198022430 3590642 0.018132501454506948 0.14355977234359488
chr4 191154276 3895500 0.02037882741372733 0.17323014886365543
chr5 180915260 3530953 0.019517165108128523 0.14847298902112926
chr6 171115067 3325036 0.019431579336026558 0.16649215057225328
chr7 159138663 3543243 0.022265129876075433 0.2651170281941599
chr8 146364022 3283561 0.022434208592600716 0.2791377815005813
chr9 141213431 2059720 0.01458586471140978 0.1534690888395316
chr10 135534747 2776902 0.020488487723373253 0.22089286216597115
chr11 135006516 2224821 0.01647936015177223 0.1639687831673098
chr12 133851895 3092589 0.023104558960483898 0.16184823683677999
chr13 115169878 1874286 0.01627409903134568 0.13572856114023468
chr14 107349540 2097652 0.019540391137214 0.15017479287536048
chr15 102531392 2268939 0.02212921287560399 0.15885023764720355
chr16 90354753 2106126 0.023309520861619755 0.16885916480126686
chr17 81195210 2699000 0.03324087714041259 0.19914801759986028
chr18 78077248 1153935 0.014779401548579171 0.23750486588850372
chr19 59128983 1587444 0.026847138568238185 0.2684433414943558
chr20 63025520 1998051 0.03170225330945306 0.19487535924146646
chr21 48129895 784607 0.016301863945475052 0.1572785764279753
chr22 51304566 576494 0.011236699673085628 0.11237361572455361
chrMT 16571 40276 2.4305111339086354 2.1607575789724214
chrX 155270560 3364202 0.021666708743756705 0.16827614826577533
chrY 59373566 222156 0.0037416651039622584 0.1755690396762351