BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716489.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 = 894,342
number of mapped reads = 639,568 (71.51%)
number of supplementary alignments = 3,206 (0.36%)
number of secondary alignments = 0
number of mapped bases = 36,401,333 bp
number of sequenced bases = 36,390,897 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 13,549
duplication rate = 1.65%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.5031
>>>>>>> ACTG content
number of A's = 9,518,506 bp (26.16%)
number of C's = 6,507,932 bp (17.88%)
number of T's = 11,413,076 bp (31.36%)
number of G's = 8,950,937 bp (24.6%)
number of N's = 446 bp (0%)
GC percentage = 42.48%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 183,319
number of insertions = 2,692
mapped reads with insertion percentage = 0.42%
number of deletions = 6,684
mapped reads with deletion percentage = 1.04%
homopolymer indels = 40.44%
>>>>>>> Coverage
mean coverageData = 0.0118X
std coverageData = 0.1347X
There is a 1.11% of reference with a coverageData >= 1X
There is a 0.05% 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 2951674 0.01184219316348263 0.20061333841037945
chr2 243199373 3074617 0.012642372231773804 0.1623632619358599
chr3 198022430 2403493 0.012137478567453192 0.11540446784445689
chr4 191154276 2333929 0.012209661477831655 0.11884854344434968
chr5 180915260 2185703 0.01208136339632157 0.11444110656534705
chr6 171115067 2102515 0.012287141260330979 0.1239432039018146
chr7 159138663 2019318 0.012689047161342558 0.15713734616328678
chr8 146364022 1853222 0.012661731856480413 0.1353819237898992
chr9 141213431 1511830 0.01070599297314715 0.12155559047288879
chr10 135534747 1729701 0.012762048391915321 0.1329462285128015
chr11 135006516 1652968 0.012243616448853476 0.12524480720942582
chr12 133851895 1642444 0.012270607001865757 0.115866225448931
chr13 115169878 1151758 0.010000514196950005 0.10408391019304652
chr14 107349540 1096573 0.010214976235575858 0.10684309631960577
chr15 102531392 1052824 0.010268308851205298 0.10677586502682877
chr16 90354753 1061776 0.0117511914398128 0.11579373443005019
chr17 81195210 985080 0.01213224277639038 0.11725387471825498
chr18 78077248 981626 0.012572497432286547 0.17000487459412103
chr19 59128983 754663 0.01276299644795176 0.1652084642302114
chr20 63025520 766025 0.012154203567062993 0.11609155977824731
chr21 48129895 478770 0.009947455734112863 0.10678340440940569
chr22 51304566 427487 0.008332338295191893 0.09462685842290582
chrMT 16571 7574 0.4570635447468469 0.7322085943420423
chrX 155270560 2066716 0.013310417634869096 0.1264653263322204
chrY 59373566 109047 0.0018366254100351661 0.05732988519978569