BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716273.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 = 475,712
number of mapped reads = 403,503 (84.82%)
number of supplementary alignments = 1,623 (0.34%)
number of secondary alignments = 0
number of mapped bases = 23,506,166 bp
number of sequenced bases = 23,498,727 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 7,113
duplication rate = 1.37%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.3685
>>>>>>> ACTG content
number of A's = 6,117,846 bp (26.03%)
number of C's = 4,014,364 bp (17.08%)
number of T's = 7,539,976 bp (32.09%)
number of G's = 5,825,884 bp (24.79%)
number of N's = 657 bp (0%)
GC percentage = 41.88%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 119,174
number of insertions = 1,772
mapped reads with insertion percentage = 0.44%
number of deletions = 4,620
mapped reads with deletion percentage = 1.14%
homopolymer indels = 42.32%
>>>>>>> Coverage
mean coverageData = 0.0076X
std coverageData = 0.1038X
There is a 0.73% of reference with a coverageData >= 1X
There is a 0.02% 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 1898995 0.007618817527439581 0.1564122489371873
chr2 243199373 1975990 0.008124979828792568 0.11623245582175717
chr3 198022430 1574528 0.0079512608748413 0.09217824915691142
chr4 191154276 1525581 0.007980888693277257 0.09446076344248933
chr5 180915260 1431980 0.007915197424473757 0.09171632829270557
chr6 171115067 1378272 0.008054650149539433 0.09862139019005896
chr7 159138663 1282868 0.008061321967999694 0.11336625582525656
chr8 146364022 1183334 0.008084869381356575 0.10594336083641416
chr9 141213431 983618 0.0069654705861512565 0.09309761017598456
chr10 135534747 1126031 0.008308061400667978 0.10577322791738399
chr11 135006516 1076476 0.007973511441477388 0.09749546898118808
chr12 133851895 1058634 0.007908995236862355 0.09210584518851926
chr13 115169878 738886 0.006415618500524938 0.08272264954037725
chr14 107349540 715751 0.006667480829447429 0.08465287939193254
chr15 102531392 676283 0.00659586285534873 0.08378962863522131
chr16 90354753 666110 0.007372163365882921 0.0901338757190996
chr17 81195210 625592 0.007704789482039643 0.09100082769090308
chr18 78077248 620766 0.007950664449648636 0.12243565061684604
chr19 59128983 460801 0.007793149427244504 0.12199878020835882
chr20 63025520 490736 0.007786306245470089 0.09072899641219047
chr21 48129895 311995 0.006482353639042844 0.08673961389940306
chr22 51304566 282398 0.00550434438915242 0.07652221390263687
chrMT 16571 1658 0.1000543117494418 0.31556009854897044
chrX 155270560 1346082 0.00866926737431745 0.09865033208318595
chrY 59373566 72801 0.001226151718763195 0.04647904231434419