BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525175.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 = 931,185 number of mapped reads = 842,348 (90.46%) number of supplementary alignments = 3,265 (0.35%) number of secondary alignments = 0 number of mapped bases = 52,488,043 bp number of sequenced bases = 52,469,516 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,450 duplication rate = 1.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1394 >>>>>>> ACTG content number of A's = 14,419,755 bp (27.48%) number of C's = 11,026,950 bp (21.02%) number of T's = 15,369,024 bp (29.29%) number of G's = 11,652,354 bp (22.21%) number of N's = 1,433 bp (0%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 253,847 number of insertions = 4,612 mapped reads with insertion percentage = 0.55% number of deletions = 11,494 mapped reads with deletion percentage = 1.36% homopolymer indels = 41.96% >>>>>>> Coverage mean coverageData = 0.017X std coverageData = 0.1864X There is a 1.59% 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 5819796 0.023349173521216623 0.3527914658756183 chr2 243199373 4455598 0.018320762693742637 0.18964429575620315 chr3 198022430 4189666 0.021157532507807324 0.15218290255036537 chr4 191154276 2942734 0.015394549688231928 0.13281287556647722 chr5 180915260 2440089 0.013487469216250747 0.121215527010573 chr6 171115067 2657757 0.015531987022510414 0.13969282170437242 chr7 159138663 3168215 0.019908518396940408 0.2624192958024977 chr8 146364022 2444657 0.016702581458167363 0.15361834048250383 chr9 141213431 1778610 0.0125951900425109 0.14568839883304743 chr10 135534747 2950490 0.02176925154108267 0.21050524115288805 chr11 135006516 2469475 0.01829152453648978 0.15897597184881387 chr12 133851895 2430784 0.01816025092509897 0.14149904456323906 chr13 115169878 1686738 0.014645652398798234 0.12597603906888177 chr14 107349540 2011102 0.018734146415531915 0.14686101113447 chr15 102531392 1471950 0.014356091059409395 0.12541895713029402 chr16 90354753 1466225 0.016227425246793603 0.1430240538210476 chr17 81195210 1076997 0.013264292314780638 0.12359836676150815 chr18 78077248 1168844 0.014970353463277804 0.2667025224116929 chr19 59128983 920808 0.015572870583618866 0.2562515689039014 chr20 63025520 1006957 0.015976972502567213 0.1331420958972142 chr21 48129895 687822 0.014290951600870934 0.12951106081598723 chr22 51304566 439052 0.008557756828115454 0.09666130013689843 chrMT 16571 3458 0.20867781063303362 0.5000990868465105 chrX 155270560 2654034 0.01709296340529718 0.1426495950307783 chrY 59373566 146185 0.0024621226220436212 0.08307311831044749