BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231814.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,293,025 number of mapped reads = 4,914,725 (92.85%) number of supplementary alignments = 32,906 (0.62%) number of secondary alignments = 0 number of mapped bases = 315,725,886 bp number of sequenced bases = 315,602,790 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 466,834 duplication rate = 7.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7524 >>>>>>> ACTG content number of A's = 81,394,422 bp (25.79%) number of C's = 57,384,233 bp (18.18%) number of T's = 101,957,950 bp (32.31%) number of G's = 74,745,724 bp (23.68%) number of N's = 120,461 bp (0.04%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 2,016,973 number of insertions = 21,087 mapped reads with insertion percentage = 0.43% number of deletions = 71,521 mapped reads with deletion percentage = 1.44% homopolymer indels = 43.82% >>>>>>> Coverage mean coverageData = 0.102X std coverageData = 1.159X There is a 7.9% of reference with a coverageData >= 1X There is a 1.52% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 30869114 0.12384769143664441 2.6360648992412314 chr2 243199373 18111573 0.07447212045238291 1.6902836493243825 chr3 198022430 36602535 0.18484034864131302 0.5460771703535305 chr4 191154276 14430578 0.07549178758627403 0.4122414821153278 chr5 180915260 18486877 0.10218528276719167 0.4243130271498029 chr6 171115067 21614829 0.12631750890761712 0.7496189198316336 chr7 159138663 21216576 0.13332131614050322 1.5672764936473025 chr8 146364022 20244570 0.13831657345409654 1.311857521826819 chr9 141213431 12496855 0.08849622101455774 0.7445682903416345 chr10 135534747 13133971 0.09690482544671737 0.8584901239969788 chr11 135006516 12304948 0.09114336377660467 0.7612116911873007 chr12 133851895 10813816 0.08078941280584784 0.39442077519837726 chr13 115169878 11796767 0.10242927408501726 0.4434280750219636 chr14 107349540 15041623 0.1401181877444468 0.538676254286427 chr15 102531392 6088609 0.05938287661207214 0.4169646512479812 chr16 90354753 7169823 0.07935191854268031 0.5030323727514313 chr17 81195210 7441637 0.09165118237886201 0.4797431691204941 chr18 78077248 5266125 0.06744762571549653 1.8959699964293042 chr19 59128983 8239105 0.1393412262815344 1.4261361548684868 chr20 63025520 6144711 0.0974956017816275 0.4540711529490276 chr21 48129895 5050385 0.1049323918117835 0.42635318032716524 chr22 51304566 2824850 0.05506040144653012 0.28302862055091327 chrMT 16571 365401 22.050630619757406 12.477038785486817 chrX 155270560 9352890 0.0602360808127439 0.47149380333340296 chrY 59373566 617718 0.010403922850111446 0.21030164183025202