BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068950.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 = 2,138,963 number of mapped reads = 1,721,125 (80.47%) number of supplementary alignments = 8,329 (0.39%) number of secondary alignments = 0 number of mapped bases = 111,656,385 bp number of sequenced bases = 111,606,613 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,799 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0614 >>>>>>> ACTG content number of A's = 29,466,706 bp (26.4%) number of C's = 19,337,976 bp (17.33%) number of T's = 36,860,754 bp (33.03%) number of G's = 25,676,877 bp (23.01%) number of N's = 264,300 bp (0.24%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,070,503 number of insertions = 10,634 mapped reads with insertion percentage = 0.61% number of deletions = 29,991 mapped reads with deletion percentage = 1.73% homopolymer indels = 47.92% >>>>>>> Coverage mean coverageData = 0.0361X std coverageData = 0.4435X There is a 3.22% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13657668 0.05479492065137122 0.9319370204876248 chr2 243199373 9911108 0.040753016250580545 0.4292599858890952 chr3 198022430 9151736 0.04621565344895525 0.2467395197581312 chr4 191154276 5408034 0.028291462336945055 0.20802413973211506 chr5 180915260 6293452 0.03478673938284697 0.20382936853264905 chr6 171115067 7538882 0.044057382743507914 0.3187202885402233 chr7 159138663 6104986 0.03836268248653063 0.6647137794012468 chr8 146364022 5929196 0.040509928047754794 0.623751978268364 chr9 141213431 4790885 0.03392655334604822 0.4073814440612521 chr10 135534747 7416507 0.05472033677090938 0.5399637234148944 chr11 135006516 3651765 0.027048805555429635 0.3049177455436963 chr12 133851895 3775029 0.028203029923483714 0.19611431462152712 chr13 115169878 1996783 0.0173377191560453 0.1397249808352247 chr14 107349540 4012207 0.03737516714091183 0.23621319477312713 chr15 102531392 1477446 0.014409694154937445 0.12887039016438084 chr16 90354753 1775740 0.019652978299879807 0.19981970389239442 chr17 81195210 1861280 0.022923519749502463 0.17883138663468723 chr18 78077248 3062976 0.03923007122382182 0.6634786324913772 chr19 59128983 1920153 0.032473973042966085 0.5848354181584944 chr20 63025520 1593403 0.025281869947284846 0.1924052426634578 chr21 48129895 1343809 0.027920463986052742 0.20906512481900352 chr22 51304566 721470 0.014062491046118585 0.1292200136388817 chrMT 16571 185149 11.173073441554523 6.987962855993239 chrX 155270560 7773351 0.0500632637635879 0.30339466242058327 chrY 59373566 303370 0.0051095128764878294 0.12437120760676111