BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716756.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 = 711,497
number of mapped reads = 631,903 (88.81%)
number of supplementary alignments = 2,494 (0.35%)
number of secondary alignments = 0
number of mapped bases = 36,445,063 bp
number of sequenced bases = 36,434,113 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 15,200
duplication rate = 1.85%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.0373
>>>>>>> ACTG content
number of A's = 9,022,943 bp (24.77%)
number of C's = 7,066,973 bp (19.4%)
number of T's = 12,048,308 bp (33.07%)
number of G's = 8,294,768 bp (22.77%)
number of N's = 1,121 bp (0%)
GC percentage = 42.16%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 187,772
number of insertions = 2,537
mapped reads with insertion percentage = 0.4%
number of deletions = 6,996
mapped reads with deletion percentage = 1.1%
homopolymer indels = 42.24%
>>>>>>> Coverage
mean coverageData = 0.0118X
std coverageData = 0.138X
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 2918668 0.011709772229614626 0.21179972684655496
chr2 243199373 3080521 0.012666648610150816 0.1762090701088049
chr3 198022430 2426392 0.012253116982757963 0.1161568907255834
chr4 191154276 2355142 0.012320634668930974 0.12003168800166214
chr5 180915260 2179578 0.012047507766895948 0.11470485932167214
chr6 171115067 2117041 0.01237203150555994 0.12763637764088945
chr7 159138663 2020771 0.012698177563550348 0.15007085610560408
chr8 146364022 1826836 0.012481455312836374 0.13420058840600202
chr9 141213431 1514431 0.010724411901018112 0.12228430045932318
chr10 135534747 1748592 0.012901429623799717 0.13589781807745294
chr11 135006516 1655956 0.012265748713936148 0.12621218566714126
chr12 133851895 1645093 0.012290397532287459 0.11677267771117604
chr13 115169878 1122434 0.009745899010156111 0.1037933868656474
chr14 107349540 1098831 0.010236010326639499 0.10713356725591945
chr15 102531392 1060641 0.010344548916296777 0.10664789120724022
chr16 90354753 1071818 0.011862331138241283 0.11650316368322887
chr17 81195210 972568 0.011978145016189995 0.11640238846013186
chr18 78077248 969631 0.012418867529757197 0.17727097687244645
chr19 59128983 765753 0.012950552523455375 0.17047367490516444
chr20 63025520 779641 0.012370243038058235 0.11742299647176768
chr21 48129895 490153 0.010183961548222783 0.1113683344524897
chr22 51304566 435746 0.008493318119092947 0.09636856230871085
chrMT 16571 2856 0.17234928489529902 0.4157140880770209
chrX 155270560 2072255 0.013346090849417945 0.12678176505236088
chrY 59373566 113715 0.0019152462562211608 0.061090980736955944