BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717055.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 = 757,209 number of mapped reads = 583,964 (77.12%) number of supplementary alignments = 2,357 (0.31%) number of secondary alignments = 0 number of mapped bases = 32,268,544 bp number of sequenced bases = 32,259,241 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,562 duplication rate = 1.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.7464 >>>>>>> ACTG content number of A's = 7,730,012 bp (23.96%) number of C's = 6,725,272 bp (20.85%) number of T's = 9,678,834 bp (30%) number of G's = 8,124,259 bp (25.18%) number of N's = 864 bp (0%) GC percentage = 46.03% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 173,984 number of insertions = 2,555 mapped reads with insertion percentage = 0.43% number of deletions = 5,431 mapped reads with deletion percentage = 0.92% homopolymer indels = 33.47% >>>>>>> Coverage mean coverageData = 0.0104X std coverageData = 0.1202X There is a 0.97% 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 3165641 0.012700634354688328 0.13948345325783384 chr2 243199373 2769705 0.011388618999441253 0.14550381525924225 chr3 198022430 2186224 0.011040284678861884 0.11395589199178756 chr4 191154276 2100390 0.010987931025932164 0.12061500857427954 chr5 180915260 1931762 0.010677717291509849 0.10850354936586437 chr6 171115067 1400359 0.008183727035562567 0.09819194305765279 chr7 159138663 1870580 0.011754403139606621 0.12834860942945966 chr8 146364022 1974637 0.013491273149080312 0.1287757627907444 chr9 141213431 1412655 0.01000368725549909 0.11058427363422955 chr10 135534747 1703693 0.012570156640348471 0.16765322346939837 chr11 135006516 1317737 0.009760543705905277 0.11463158960609375 chr12 133851895 1553767 0.011608106108621025 0.11492745772056857 chr13 115169878 571241 0.004959986151934623 0.07561181775651213 chr14 107349540 1031236 0.009606338322455783 0.10662067407374785 chr15 102531392 660252 0.006439510740281377 0.08648699393432897 chr16 90354753 885305 0.009798101047323985 0.10959622194075884 chr17 81195210 1234281 0.015201401659038754 0.13776554755767176 chr18 78077248 859218 0.011004716764607278 0.12475572165704453 chr19 59128983 872969 0.014763808807602865 0.1443731390540657 chr20 63025520 825087 0.01309131602563533 0.1276593335611374 chr21 48129895 431789 0.008971326448977293 0.11281916035135084 chr22 51304566 349922 0.00682048455492246 0.08825525504997027 chrMT 16571 16228 0.9793011888238489 1.264011455539416 chrX 155270560 1036835 0.006677601987137806 0.09269882089731017 chrY 59373566 107031 0.0018026709057697495 0.07128126086315476