BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9717045.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 = 2,593,344
number of mapped reads = 2,395,678 (92.38%)
number of supplementary alignments = 67,904 (2.62%)
number of secondary alignments = 0
number of mapped bases = 177,099,078 bp
number of sequenced bases = 177,036,165 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 82,596
duplication rate = 2.28%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.757
>>>>>>> ACTG content
number of A's = 45,337,298 bp (25.61%)
number of C's = 36,036,147 bp (20.36%)
number of T's = 53,017,736 bp (29.95%)
number of G's = 42,624,450 bp (24.08%)
number of N's = 20,534 bp (0.01%)
GC percentage = 44.43%
>>>>>>> Mismatches and indels
general error rate = 0.0076
number of mismatches = 1,319,998
number of insertions = 15,101
mapped reads with insertion percentage = 0.62%
number of deletions = 36,116
mapped reads with deletion percentage = 1.49%
homopolymer indels = 39.42%
>>>>>>> Coverage
mean coverageData = 0.0572X
std coverageData = 0.4606X
There is a 4.83% of reference with a coverageData >= 1X
There is a 0.63% of reference with a coverageData >= 2X
There is a 0.12% 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 14009146 0.05620505956532802 0.6298424874345948
chr2 243199373 14409933 0.059251522001251215 0.7330572105269049
chr3 198022430 13905344 0.0702210552612651 0.3166952070156857
chr4 191154276 7605042 0.039784838503952695 0.25074172898913455
chr5 180915260 10911210 0.06031116446451228 0.2863125021291329
chr6 171115067 13355907 0.07805219747247623 0.38279144337066434
chr7 159138663 9626177 0.060489241385671313 0.6522056093454757
chr8 146364022 13446714 0.09187171694420915 0.598323273247736
chr9 141213431 7948735 0.0562888030105295 0.428538738637973
chr10 135534747 8097547 0.05974517368597737 0.4509643153842752
chr11 135006516 6420905 0.047559963698344754 0.36547087719075694
chr12 133851895 6806848 0.05085357962246257 0.26017844467497936
chr13 115169878 6618824 0.05747009647783077 0.27371858679714517
chr14 107349540 4279904 0.03986886203704273 0.2674526877628388
chr15 102531392 3566802 0.034787414180429736 0.21356647419394326
chr16 90354753 4312895 0.047732906756991524 0.2926510660840142
chr17 81195210 6185102 0.07617570051238244 0.35825872239258
chr18 78077248 5629466 0.07210123492057507 0.8791799774987631
chr19 59128983 3358796 0.05680456232436807 0.5845809913283535
chr20 63025520 3472531 0.05509722093526559 0.3101475528607513
chr21 48129895 3854258 0.08008033260824692 0.34468692744441654
chr22 51304566 2807796 0.05472799438552896 0.2728932296440071
chrMT 16571 18488 1.1156840263110253 1.4549205580702294
chrX 155270560 6024220 0.03879821132866398 0.32012706157822285
chrY 59373566 426488 0.007183129273387419 0.21646308766168695