BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716469.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 = 590,680
number of mapped reads = 539,564 (91.35%)
number of supplementary alignments = 1,743 (0.3%)
number of secondary alignments = 0
number of mapped bases = 31,109,230 bp
number of sequenced bases = 31,100,290 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 11,581
duplication rate = 1.51%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.2254
>>>>>>> ACTG content
number of A's = 7,578,930 bp (24.37%)
number of C's = 6,011,167 bp (19.33%)
number of T's = 9,814,312 bp (31.56%)
number of G's = 7,695,287 bp (24.74%)
number of N's = 594 bp (0%)
GC percentage = 44.07%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 156,721
number of insertions = 1,963
mapped reads with insertion percentage = 0.36%
number of deletions = 5,568
mapped reads with deletion percentage = 1.02%
homopolymer indels = 42.94%
>>>>>>> Coverage
mean coverageData = 0.01X
std coverageData = 0.1297X
There is a 0.95% 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 2641168 0.010596434983405718 0.17683115408215014
chr2 243199373 2467493 0.010145967769415261 0.1870344447648533
chr3 198022430 1797111 0.009075290107287342 0.09911344371242445
chr4 191154276 1939943 0.01014857235001115 0.1128887798066783
chr5 180915260 1775712 0.00981515876549054 0.10260038726615643
chr6 171115067 1656760 0.009682139796608326 0.11037635724439042
chr7 159138663 1784555 0.011213836828577604 0.1521211918147923
chr8 146364022 1448824 0.009898771434417128 0.1571115832392391
chr9 141213431 1037941 0.007350157790585798 0.09862751523599879
chr10 135534747 1382420 0.010199746047410262 0.1337900076145394
chr11 135006516 1116283 0.008268363876599853 0.10324260523091572
chr12 133851895 1551630 0.011592140701482036 0.11202724701339037
chr13 115169878 936224 0.008129069998667533 0.09363394968323355
chr14 107349540 1048603 0.009768118242518786 0.10220371379860692
chr15 102531392 1135491 0.011074569240218645 0.10919631670943933
chr16 90354753 1085755 0.012016578696197643 0.11581881402602773
chr17 81195210 1383024 0.01703332006900407 0.13732247718234578
chr18 78077248 590738 0.007566070976272115 0.1309172595254905
chr19 59128983 796984 0.01347873681507426 0.15317892579977901
chr20 63025520 1039488 0.016493128497789465 0.1349070635429102
chr21 48129895 397595 0.008260874036812256 0.10256546463400254
chr22 51304566 293206 0.005715007900076574 0.0776552287448997
chrMT 16571 1617 0.09758010983042664 0.33333249513741897
chrX 155270560 1681682 0.010830655856461134 0.11163245889054252
chrY 59373566 118983 0.0020039726096290054 0.0893841613432717