BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716800.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 = 1,336,943
number of mapped reads = 1,219,115 (91.19%)
number of supplementary alignments = 6,283 (0.47%)
number of secondary alignments = 0
number of mapped bases = 71,226,792 bp
number of sequenced bases = 71,206,194 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 42,627
duplication rate = 2.78%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9839
>>>>>>> ACTG content
number of A's = 17,511,068 bp (24.59%)
number of C's = 13,784,579 bp (19.36%)
number of T's = 22,426,091 bp (31.49%)
number of G's = 17,483,417 bp (24.55%)
number of N's = 1,039 bp (0%)
GC percentage = 43.91%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 350,715
number of insertions = 5,384
mapped reads with insertion percentage = 0.44%
number of deletions = 13,010
mapped reads with deletion percentage = 1.06%
homopolymer indels = 41.93%
>>>>>>> Coverage
mean coverageData = 0.023X
std coverageData = 0.209X
There is a 2.07% of reference with a coverageData >= 1X
There is a 0.18% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 5770917 0.02315306969686547 0.31560813421526157
chr2 243199373 6010001 0.024712238875714537 0.27519046369887123
chr3 198022430 4836585 0.024424430101175912 0.171359129855001
chr4 191154276 4562413 0.023867700453637772 0.1792432409882616
chr5 180915260 4284697 0.02368344715642008 0.16879953393450348
chr6 171115067 4038637 0.023601878378132535 0.19147206570360648
chr7 159138663 3879659 0.024379110185184853 0.24612456824907214
chr8 146364022 3497467 0.023895674307173657 0.19147761639604632
chr9 141213431 2895660 0.02050555658547805 0.18029972596343813
chr10 135534747 3426159 0.025278823887132058 0.20977124100115205
chr11 135006516 3185876 0.023597942487457422 0.1962634504562488
chr12 133851895 3357591 0.025084374038933106 0.17464079980869965
chr13 115169878 2130535 0.018499064486288682 0.14836337071585093
chr14 107349540 2156944 0.020092717677225258 0.16049062820891338
chr15 102531392 2055681 0.0200492840280565 0.15924214202768208
chr16 90354753 2085121 0.023077048309788416 0.17421290072144738
chr17 81195210 2028212 0.024979453837239905 0.1800532431627723
chr18 78077248 1853727 0.023742217451106884 0.28203892221016325
chr19 59128983 1579593 0.02671436104355118 0.2584431214916868
chr20 63025520 1588305 0.025200982078370793 0.1754116056491735
chr21 48129895 941394 0.019559444291328706 0.1630390965641169
chr22 51304566 882227 0.017195876873804954 0.14358374445045188
chrMT 16571 5738 0.34626757588558327 0.6894468691489539
chrX 155270560 3961520 0.025513658223426258 0.18691828418340078
chrY 59373566 212133 0.0035728526058212504 0.09381510865168571