BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6236115.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,305,841
number of mapped reads = 1,096,025 (83.93%)
number of supplementary alignments = 8,262 (0.63%)
number of secondary alignments = 0
number of mapped bases = 73,843,960 bp
number of sequenced bases = 73,807,100 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 73,659
duplication rate = 5.19%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 40.2963
>>>>>>> ACTG content
number of A's = 20,743,935 bp (28.11%)
number of C's = 13,392,390 bp (18.15%)
number of T's = 23,547,032 bp (31.9%)
number of G's = 16,078,634 bp (21.78%)
number of N's = 45,109 bp (0.06%)
GC percentage = 39.93%
>>>>>>> Mismatches and indels
general error rate = 0.0085
number of mismatches = 620,011
number of insertions = 5,539
mapped reads with insertion percentage = 0.5%
number of deletions = 20,964
mapped reads with deletion percentage = 1.89%
homopolymer indels = 47.1%
>>>>>>> Coverage
mean coverageData = 0.0239X
std coverageData = 0.3607X
There is a 1.69% of reference with a coverageData >= 1X
There is a 0.45% of reference with a coverageData >= 2X
There is a 0.13% of reference with a coverageData >= 3X
There is a 0.04% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.01% 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 3683503 0.014778310221341434 0.7374219501305497
chr2 243199373 12538322 0.05155573324607214 0.5284524604705979
chr3 198022430 10608169 0.05357054248854536 0.3090000150466398
chr4 191154276 1054426 0.0055160994672177775 0.10437621105214145
chr5 180915260 8107344 0.04481293617796531 0.2871972364966143
chr6 171115067 2075356 0.01212842350112863 0.14822605907574796
chr7 159138663 2328968 0.014634834527923614 0.4834273455165448
chr8 146364022 2326712 0.01589674817763617 0.4404283715355799
chr9 141213431 3500717 0.024790255255535857 0.33997781460293774
chr10 135534747 668731 0.004934018875617187 0.1350063715443881
chr11 135006516 784954 0.005814193442337258 0.189143824879274
chr12 133851895 2716782 0.02029692594191513 0.19446233408113098
chr13 115169878 378048 0.0032825249671619866 0.07161664814523679
chr14 107349540 6133333 0.057134227123842356 0.3206937791567552
chr15 102531392 349994 0.0034135301703501694 0.07731132188674297
chr16 90354753 1880347 0.020810714849721298 0.21729994393446375
chr17 81195210 1506526 0.018554370387120128 0.17748693747431335
chr18 78077248 2996398 0.038377351619770204 0.46617021688447574
chr19 59128983 2861239 0.04838978881135162 0.46702662977686515
chr20 63025520 2811386 0.0446071051853281 0.2842059092325677
chr21 48129895 2531370 0.052594546487167694 0.31094437498892846
chr22 51304566 772741 0.015061836796358438 0.15987814982091758
chrMT 16571 15155 0.9145495142115745 1.318917579889447
chrX 155270560 1054943 0.006794224223832258 0.15874968874927164
chrY 59373566 158496 0.002669470787723951 0.08356979068980276