BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716523.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 = 3,013,977
number of mapped reads = 2,807,503 (93.15%)
number of supplementary alignments = 13,337 (0.44%)
number of secondary alignments = 0
number of mapped bases = 164,590,210 bp
number of sequenced bases = 164,543,164 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 147,652
duplication rate = 3.99%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.3084
>>>>>>> ACTG content
number of A's = 42,361,115 bp (25.74%)
number of C's = 33,746,227 bp (20.51%)
number of T's = 49,902,870 bp (30.33%)
number of G's = 38,528,399 bp (23.42%)
number of N's = 4,553 bp (0%)
GC percentage = 43.92%
>>>>>>> Mismatches and indels
general error rate = 0.0049
number of mismatches = 790,125
number of insertions = 9,754
mapped reads with insertion percentage = 0.35%
number of deletions = 29,795
mapped reads with deletion percentage = 1.05%
homopolymer indels = 43.72%
>>>>>>> Coverage
mean coverageData = 0.0532X
std coverageData = 0.4359X
There is a 4.48% of reference with a coverageData >= 1X
There is a 0.61% of reference with a coverageData >= 2X
There is a 0.11% of reference with a coverageData >= 3X
There is a 0.03% of reference with a coverageData >= 4X
There is a 0.01% 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 18845459 0.0756084736093797 0.8450882399697266
chr2 243199373 14277860 0.058708457278794056 0.5570411105294837
chr3 198022430 13568292 0.06851896525055268 0.3071611770872217
chr4 191154276 7800789 0.04080886477266143 0.25405367776710025
chr5 180915260 7382757 0.040807817980639115 0.2382607430779745
chr6 171115067 11582435 0.06768799032758466 0.4360478946228603
chr7 159138663 9583402 0.06022045063932704 0.5554912982687729
chr8 146364022 10940094 0.07474578691203225 0.375304131372282
chr9 141213431 6198981 0.04389795613704762 0.36622831460666166
chr10 135534747 8671466 0.06397965239127941 0.4616421799039513
chr11 135006516 5613379 0.04157857832580466 0.3391260566897423
chr12 133851895 7387716 0.05519321187047819 0.2848817466586425
chr13 115169878 3787334 0.032884761760362376 0.21246001397386466
chr14 107349540 3673042 0.03421572183728035 0.2479715303280741
chr15 102531392 5040254 0.04915815441187027 0.26002861001853456
chr16 90354753 3547369 0.039260458163169344 0.2743628744595571
chr17 81195210 3685975 0.04539645873198678 0.26315381972900675
chr18 78077248 3270789 0.04189170448220716 0.7000046563168378
chr19 59128983 3545102 0.059955402919749184 0.5576823487178415
chr20 63025520 2601126 0.04127099625675441 0.23877168477663274
chr21 48129895 1530053 0.03179007558607805 0.23785461259266794
chr22 51304566 2699900 0.05262494570171396 0.2691260655987047
chrMT 16571 55002 3.319172047552954 2.6886846501720654
chrX 155270560 8909314 0.05737928683969453 0.33066428330113035
chrY 59373566 392320 0.006607654322127123 0.14238161163930788