BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716794.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 = 633,241 number of mapped reads = 485,971 (76.74%) number of supplementary alignments = 652 (0.1%) number of secondary alignments = 0 number of mapped bases = 25,696,621 bp number of sequenced bases = 25,690,437 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,548 duplication rate = 5.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.955 >>>>>>> ACTG content number of A's = 5,033,438 bp (19.59%) number of C's = 4,807,837 bp (18.71%) number of T's = 8,614,154 bp (33.53%) number of G's = 7,234,563 bp (28.16%) number of N's = 445 bp (0%) GC percentage = 46.88% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 166,512 number of insertions = 1,635 mapped reads with insertion percentage = 0.34% number of deletions = 3,623 mapped reads with deletion percentage = 0.74% homopolymer indels = 39.67% >>>>>>> Coverage mean coverageData = 0.0083X std coverageData = 0.1068X There is a 0.74% of reference with a coverageData >= 1X There is a 0.07% 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 2691853 0.010799784526915983 0.12078527424437271 chr2 243199373 2115011 0.008696613703851943 0.1377474065807471 chr3 198022430 1746802 0.008821233029005856 0.10332580202980368 chr4 191154276 1629860 0.008526411410226576 0.10284529963589852 chr5 180915260 1558915 0.008616824252415192 0.10324020663022802 chr6 171115067 1069066 0.006247643873464398 0.09319018992247 chr7 159138663 1298297 0.008158275151526189 0.10192128250911887 chr8 146364022 1547026 0.010569715008241574 0.11590491098892963 chr9 141213431 1147109 0.008123228731691958 0.10363496228339411 chr10 135534747 1349465 0.009956598067062464 0.11737466822375302 chr11 135006516 1101774 0.00816089498969072 0.10412660669308053 chr12 133851895 1253784 0.009366949941201803 0.10711053073681295 chr13 115169878 401866 0.0034893325145312734 0.06647116994763631 chr14 107349540 826790 0.0077018494909246935 0.09713205382875123 chr15 102531392 543383 0.005299674464577638 0.08083989932354495 chr16 90354753 731237 0.008092955552653661 0.1022001587609922 chr17 81195210 1083251 0.013341316562885914 0.13305928540349243 chr18 78077248 575256 0.0073677801758586575 0.10043188824961323 chr19 59128983 742015 0.012549091196105977 0.1410603023099978 chr20 63025520 764034 0.012122613189070078 0.12863007196975063 chr21 48129895 390834 0.008120400013338903 0.10384789522308943 chr22 51304566 324068 0.006316552799608518 0.09043063745036699 chrMT 16571 11048 0.6667068975921792 1.0081105235890178 chrX 155270560 731009 0.00470796910888967 0.07557302803223999 chrY 59373566 62868 0.0010588550467054648 0.037907713877633566