BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237848.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 = 1,908,265 number of mapped reads = 1,394,531 (73.08%) number of supplementary alignments = 6,054 (0.32%) number of secondary alignments = 0 number of mapped bases = 85,260,027 bp number of sequenced bases = 85,198,930 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,740 duplication rate = 4.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1982 >>>>>>> ACTG content number of A's = 23,175,369 bp (27.2%) number of C's = 15,099,986 bp (17.72%) number of T's = 25,959,414 bp (30.47%) number of G's = 20,894,539 bp (24.52%) number of N's = 69,622 bp (0.08%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 923,211 number of insertions = 8,501 mapped reads with insertion percentage = 0.61% number of deletions = 37,912 mapped reads with deletion percentage = 2.68% homopolymer indels = 48.49% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 0.2996X There is a 2.12% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 7539247 0.03024765583231987 0.3581916322637862 chr2 243199373 7328667 0.030134399236300662 0.3951215815286349 chr3 198022430 6065581 0.030630777533635963 0.2544301228831997 chr4 191154276 5352653 0.02800174347133098 0.2380295591727175 chr5 180915260 4725149 0.026118023432628073 0.2200137588079824 chr6 171115067 4616937 0.02698147557047095 0.25384014269980143 chr7 159138663 4980881 0.03129899991682097 0.4406764841466571 chr8 146364022 4511770 0.030825676545018693 0.32573634849140737 chr9 141213431 3492439 0.024731634769216818 0.30894033413840827 chr10 135534747 3695866 0.02726877115873467 0.280955920875796 chr11 135006516 3567966 0.026428102181379157 0.3479110742070303 chr12 133851895 4793679 0.03581330693898656 0.2766933594627314 chr13 115169878 2924715 0.025394791162321108 0.2340693706254509 chr14 107349540 2429823 0.02263468478765722 0.23473134619810887 chr15 102531392 2580697 0.025169823111345257 0.22711809921072135 chr16 90354753 2253808 0.02494398938813988 0.2463466643422488 chr17 81195210 2024531 0.024934118650595274 0.23611260814020926 chr18 78077248 2181261 0.0279372167420655 0.445128645707697 chr19 59128983 1551309 0.026236016946207242 0.2883981668752063 chr20 63025520 1723372 0.027344034606933826 0.2378415303859733 chr21 48129895 1060607 0.02203634560183437 0.222932130342613 chr22 51304566 876464 0.017083547690472618 0.18199466846234202 chrMT 16571 55771 3.365578420131555 3.6875456116860486 chrX 155270560 4627321 0.02980166362509416 0.258517915220439 chrY 59373566 299513 0.005044551307563369 0.12061877130391552