BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230377.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 = 4,899,487 number of mapped reads = 4,141,080 (84.52%) number of supplementary alignments = 43,948 (0.9%) number of secondary alignments = 0 number of mapped bases = 288,574,702 bp number of sequenced bases = 288,433,362 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 409,809 duplication rate = 7.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7686 >>>>>>> ACTG content number of A's = 86,694,960 bp (30.06%) number of C's = 56,886,950 bp (19.72%) number of T's = 85,823,773 bp (29.76%) number of G's = 58,866,546 bp (20.41%) number of N's = 161,133 bp (0.06%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 2,612,629 number of insertions = 30,291 mapped reads with insertion percentage = 0.72% number of deletions = 80,277 mapped reads with deletion percentage = 1.91% homopolymer indels = 45.18% >>>>>>> Coverage mean coverageData = 0.0932X std coverageData = 1.3181X There is a 2.98% of reference with a coverageData >= 1X There is a 1.7% of reference with a coverageData >= 2X There is a 1.17% of reference with a coverageData >= 3X There is a 0.84% of reference with a coverageData >= 4X There is a 0.61% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 9167793 0.036781424909669534 2.0678495200767086 chr2 243199373 6336975 0.026056707802449803 1.4972273144572816 chr3 198022430 3075727 0.015532215214205785 0.28745751857190577 chr4 191154276 18054255 0.09444860652764053 1.3550804088885298 chr5 180915260 24412427 0.13493846234972107 0.9180578181941673 chr6 171115067 34644791 0.20246487704089786 1.8567454539745891 chr7 159138663 5627535 0.03536246248342554 0.6438269753609974 chr8 146364022 13543946 0.09253603320630258 0.8791499548645446 chr9 141213431 8359440 0.05919720199985793 1.0765303072112478 chr10 135534747 8496907 0.06269172435906786 1.9405974671778767 chr11 135006516 17554309 0.13002564261416835 0.982123291238101 chr12 133851895 12406793 0.09269045462524084 0.7580521171120147 chr13 115169878 24826041 0.2155601918758653 1.161444168886314 chr14 107349540 7958977 0.07414076483234115 0.8329065792396456 chr15 102531392 4933701 0.04811893122449756 0.5367638643585197 chr16 90354753 2659988 0.029439381014079027 0.7787393424830253 chr17 81195210 4022077 0.04953589010977372 0.6495541926087962 chr18 78077248 8672529 0.11107626385602115 2.443442736021333 chr19 59128983 8138785 0.13764459639023388 1.5486713936646646 chr20 63025520 10341652 0.16408673819747938 1.1156509136673003 chr21 48129895 1374640 0.02856104298586149 1.0699854424335198 chr22 51304566 477695 0.009310964642016462 0.19582680482321044 chrMT 16571 7299 0.44046828797296483 1.1470217576454478 chrX 155270560 52164578 0.3359592314215908 1.5687764554551107 chrY 59373566 1315842 0.022162084723023036 1.3248494795826293