BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238080.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 = 1,736,020 number of mapped reads = 1,265,656 (72.91%) number of supplementary alignments = 10,321 (0.59%) number of secondary alignments = 0 number of mapped bases = 77,624,924 bp number of sequenced bases = 77,587,954 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 208,633 duplication rate = 13.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8554 >>>>>>> ACTG content number of A's = 20,093,609 bp (25.9%) number of C's = 13,340,214 bp (17.19%) number of T's = 25,591,547 bp (32.98%) number of G's = 18,558,821 bp (23.92%) number of N's = 3,763 bp (0%) GC percentage = 41.11% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 592,492 number of insertions = 6,273 mapped reads with insertion percentage = 0.49% number of deletions = 23,118 mapped reads with deletion percentage = 1.81% homopolymer indels = 46.67% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.3257X There is a 1.54% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.09% 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% 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 5688354 0.02282182478494206 0.5209031510248877 chr2 243199373 6970127 0.02866013556704359 0.44355448682089665 chr3 198022430 4200823 0.021213874610063112 0.2236702040991281 chr4 191154276 4119994 0.02155324006458532 0.23462077326270311 chr5 180915260 5349248 0.029567699264285388 0.26179806037148795 chr6 171115067 4755993 0.027794121718106798 0.33511858763874347 chr7 159138663 3883151 0.02440105331285836 0.3161957170738251 chr8 146364022 4121439 0.02815882580761548 0.31902262343660054 chr9 141213431 3251024 0.023022059424361696 0.27622369796862434 chr10 135534747 3543175 0.026142189205547416 0.3085992707207332 chr11 135006516 3263199 0.024170677806395657 0.27093039017983717 chr12 133851895 3091168 0.023093942749185584 0.24056956225843706 chr13 115169878 2754616 0.02391785115896363 0.24781054385515436 chr14 107349540 2820994 0.0262785848919334 0.2516335050606978 chr15 102531392 2808397 0.02739060638131198 0.25433299544526144 chr16 90354753 1884891 0.020861005507922754 0.22366831862377903 chr17 81195210 2285374 0.028146660375655164 0.2621371654221568 chr18 78077248 1835185 0.023504734695567138 0.5631904732109224 chr19 59128983 1382166 0.023375440095088393 0.3862385447792801 chr20 63025520 1925554 0.030551973232430293 0.2681291731562189 chr21 48129895 1085737 0.022558474312067374 0.23920782194598797 chr22 51304566 1076008 0.020972948099785116 0.21357432732730106 chrMT 16571 55565 3.3531470641482106 3.4830288635113686 chrX 155270560 5187314 0.03340822626001993 0.2947802680637579 chrY 59373566 285428 0.004807324525530436 0.12820866109320103