BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716932.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 = 1,039,982
number of mapped reads = 948,709 (91.22%)
number of supplementary alignments = 3,201 (0.31%)
number of secondary alignments = 0
number of mapped bases = 54,939,751 bp
number of sequenced bases = 54,921,876 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 35,012
duplication rate = 2.73%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.5387
>>>>>>> ACTG content
number of A's = 12,864,435 bp (23.42%)
number of C's = 10,707,537 bp (19.5%)
number of T's = 18,207,828 bp (33.15%)
number of G's = 13,141,018 bp (23.93%)
number of N's = 1,058 bp (0%)
GC percentage = 43.42%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 279,972
number of insertions = 4,268
mapped reads with insertion percentage = 0.45%
number of deletions = 11,058
mapped reads with deletion percentage = 1.15%
homopolymer indels = 43.02%
>>>>>>> Coverage
mean coverageData = 0.0177X
std coverageData = 0.1924X
There is a 1.63% 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 4597337 0.018444636091799346 0.25417143451185287
chr2 243199373 4335518 0.017827011420790136 0.28713874884875357
chr3 198022430 3150469 0.015909657304983078 0.1357896898602758
chr4 191154276 3358012 0.017567025285900484 0.1775133701638121
chr5 180915260 3073289 0.01698745036764726 0.13897105788585243
chr6 171115067 2862396 0.016727901582155823 0.15085454256615521
chr7 159138663 3070952 0.019297334425889955 0.22027081921330557
chr8 146364022 2903369 0.019836630343487007 0.25496203782086213
chr9 141213431 1834473 0.012990782725192761 0.13905753443833835
chr10 135534747 2486596 0.018346557285417002 0.22586918378635448
chr11 135006516 1968100 0.014577814895986205 0.15153096876714794
chr12 133851895 2720853 0.02032734015457906 0.15303558349206134
chr13 115169878 1622301 0.014086157146055153 0.12764728159019118
chr14 107349540 1849130 0.017225318338578814 0.14187151085184346
chr15 102531392 2030462 0.019803320333347273 0.15217939944356737
chr16 90354753 1913893 0.021181984748494635 0.16039809378715175
chr17 81195210 2428922 0.029914597178823728 0.19249832828470614
chr18 78077248 1022877 0.013100833164611539 0.20222086094230116
chr19 59128983 1464836 0.02477357001049722 0.2281183967678462
chr20 63025520 1870656 0.02968092924897724 0.1909252346450873
chr21 48129895 705196 0.014651933065717264 0.16248951563945915
chr22 51304566 551061 0.01074097381507915 0.11107084087622057
chrMT 16571 3557 0.21465210307163116 0.4802214747996404
chrX 155270560 2871499 0.018493518668316774 0.151773300016585
chrY 59373566 243997 0.004109522409349642 0.2010319248710348