BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717059.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 = 402,147 number of mapped reads = 368,590 (91.66%) number of supplementary alignments = 1,332 (0.33%) number of secondary alignments = 0 number of mapped bases = 21,063,351 bp number of sequenced bases = 21,057,360 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,910 duplication rate = 1.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5362 >>>>>>> ACTG content number of A's = 5,125,307 bp (24.34%) number of C's = 3,672,169 bp (17.44%) number of T's = 6,698,418 bp (31.81%) number of G's = 5,561,024 bp (26.41%) number of N's = 442 bp (0%) GC percentage = 43.85% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 106,938 number of insertions = 1,329 mapped reads with insertion percentage = 0.36% number of deletions = 3,592 mapped reads with deletion percentage = 0.97% homopolymer indels = 44.52% >>>>>>> Coverage mean coverageData = 0.0068X std coverageData = 0.0985X There is a 0.65% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 1671156 0.006704721510001775 0.12508619387520625 chr2 243199373 1812488 0.007452683687634343 0.12887746746146864 chr3 198022430 1405040 0.0070953578339585065 0.08707403694561965 chr4 191154276 1382896 0.0072344497279255215 0.0923557748732519 chr5 180915260 1255997 0.0069424602435416444 0.08578641553140923 chr6 171115067 1179218 0.006891374445711434 0.08826679197683046 chr7 159138663 1170489 0.007355151651613411 0.10592027728217158 chr8 146364022 1043730 0.0071310557453798315 0.11113677838900649 chr9 141213431 872104 0.0061757864944163845 0.08746090256394726 chr10 135534747 1008965 0.007444327173163941 0.10960123644569231 chr11 135006516 940214 0.006964212008848521 0.09167951778515801 chr12 133851895 942630 0.007042335859346631 0.08632393781725588 chr13 115169878 607469 0.005274547568766201 0.07463932990735243 chr14 107349540 646003 0.006017752847380623 0.08075323455495814 chr15 102531392 610409 0.005953386451634247 0.07972402010319952 chr16 90354753 617626 0.006835567355266856 0.08804002638832362 chr17 81195210 614425 0.0075672567384209 0.09148434480488167 chr18 78077248 555353 0.007112865965767646 0.1134282074421275 chr19 59128983 440837 0.007455514666978121 0.10889008980602069 chr20 63025520 445826 0.007073737749406907 0.08735325326509114 chr21 48129895 286243 0.005947301567975579 0.08446583293737583 chr22 51304566 258289 0.005034425201063001 0.07328176546180776 chrMT 16571 3857 0.2327560195522298 0.4960321733504754 chrX 155270560 1204761 0.007759107714946091 0.0938952441860362 chrY 59373566 87326 0.0014707892060921521 0.0689548539088545