BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231729.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 = 5,125,664 number of mapped reads = 4,700,602 (91.71%) number of supplementary alignments = 54,450 (1.06%) number of secondary alignments = 0 number of mapped bases = 323,478,057 bp number of sequenced bases = 323,366,899 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 817,429 duplication rate = 8.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2377 >>>>>>> ACTG content number of A's = 84,481,735 bp (26.13%) number of C's = 59,216,254 bp (18.31%) number of T's = 90,776,318 bp (28.07%) number of G's = 88,821,055 bp (27.47%) number of N's = 71,537 bp (0.02%) GC percentage = 45.78% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 2,038,998 number of insertions = 22,237 mapped reads with insertion percentage = 0.47% number of deletions = 67,795 mapped reads with deletion percentage = 1.43% homopolymer indels = 47.48% >>>>>>> Coverage mean coverageData = 0.1045X std coverageData = 45.6657X There is a 4.55% of reference with a coverageData >= 1X There is a 2.28% of reference with a coverageData >= 2X There is a 1.2% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 22867805 0.09174623079474695 1.968373778045712 chr2 243199373 51499886 0.2117599456146624 162.8897995567933 chr3 198022430 23796423 0.12017034130931531 0.6321763823608345 chr4 191154276 22310616 0.11671523372043219 0.6663566033996207 chr5 180915260 18744470 0.10360911511831561 0.5936358675990198 chr6 171115067 15706398 0.09178851561914182 0.6768114337008665 chr7 159138663 15832667 0.09948975755816171 1.0885042291768212 chr8 146364022 16936899 0.1157176385874392 1.416162622369855 chr9 141213431 13767519 0.09749440193121574 0.8874204707164969 chr10 135534747 13619294 0.10048562675960873 0.8283701627698973 chr11 135006516 13111630 0.0971184975990344 1.036765937345427 chr12 133851895 11474609 0.08572616024599428 0.5704632755225926 chr13 115169878 7826192 0.06795346262327377 0.4668248359459611 chr14 107349540 9268321 0.0863377803016203 0.7127987478408309 chr15 102531392 9143627 0.08917880486787891 0.5482133545702075 chr16 90354753 6808589 0.07535396616047414 0.5798352100762082 chr17 81195210 9277266 0.11425878447755723 0.7074375429554088 chr18 78077248 8219887 0.10527890276050714 1.7266243860655774 chr19 59128983 6555748 0.11087198979897896 1.364097194013643 chr20 63025520 6903600 0.1095365813721172 0.6452107058438272 chr21 48129895 3563997 0.07404954862253492 0.6437982634438766 chr22 51304566 5094569 0.09930049890686143 0.6370294116228533 chrMT 16571 38256 2.308611429605938 3.240713150213666 chrX 155270560 8745224 0.05632248637475127 0.5336629705966789 chrY 59373566 2364565 0.039825214473390394 0.4635993777681436