BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716370.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 = 2,227,011
number of mapped reads = 2,095,819 (94.11%)
number of supplementary alignments = 42,621 (1.91%)
number of secondary alignments = 0
number of mapped bases = 167,036,233 bp
number of sequenced bases = 166,959,900 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 98,195
duplication rate = 3.28%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.6839
>>>>>>> ACTG content
number of A's = 43,230,509 bp (25.89%)
number of C's = 32,621,792 bp (19.54%)
number of T's = 49,448,669 bp (29.62%)
number of G's = 41,647,468 bp (24.94%)
number of N's = 11,462 bp (0.01%)
GC percentage = 44.48%
>>>>>>> Mismatches and indels
general error rate = 0.0065
number of mismatches = 1,053,594
number of insertions = 13,429
mapped reads with insertion percentage = 0.63%
number of deletions = 39,723
mapped reads with deletion percentage = 1.86%
homopolymer indels = 44.45%
>>>>>>> Coverage
mean coverageData = 0.054X
std coverageData = 0.5242X
There is a 4.53% of reference with a coverageData >= 1X
There is a 0.6% 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 0.01% 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 16262267 0.06524463985187022 1.198395273343743
chr2 243199373 13625117 0.05602447420783441 0.5235501811122835
chr3 198022430 10612671 0.053593277286820486 0.26155522220718025
chr4 191154276 10540903 0.05514343294104496 0.3612315793664026
chr5 180915260 9624245 0.05319753015859469 0.26381281869559825
chr6 171115067 9115029 0.05326841849642615 0.2875991938322432
chr7 159138663 8816088 0.05539878137596267 0.6169661342400402
chr8 146364022 8213787 0.05611889375382155 0.5731524406588057
chr9 141213431 6811478 0.048235341013702866 0.41385170535338645
chr10 135534747 7831574 0.057782776545117244 0.5209299811803345
chr11 135006516 9317272 0.06901349857809826 0.5058227515033569
chr12 133851895 7233403 0.0540403481026548 0.26638035287022815
chr13 115169878 5814732 0.05048830563144297 0.2571417820344564
chr14 107349540 4828895 0.04498291282850397 0.2617952781889101
chr15 102531392 4722154 0.04605568994908408 0.2428744582666469
chr16 90354753 3771765 0.04174395784137665 0.26473904737154674
chr17 81195210 5188983 0.063907501440048 0.3526817393052717
chr18 78077248 4339057 0.05557389778902043 0.699044448043072
chr19 59128983 3263184 0.05518755497621192 0.7800372809087616
chr20 63025520 3377322 0.053586578896929374 0.2854988762053448
chr21 48129895 2227954 0.046290439652943355 0.3083381259716908
chr22 51304566 1911033 0.037248789903027345 0.22254036127325938
chrMT 16571 27494 1.6591635990585964 1.61241314423326
chrX 155270560 9030458 0.05815949913492938 0.33354105849770255
chrY 59373566 529368 0.008915886911694001 0.30597725655821734