BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013238.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 = 1,633,965 number of mapped reads = 1,479,659 (90.56%) number of supplementary alignments = 8,121 (0.5%) number of secondary alignments = 0 number of mapped bases = 99,006,966 bp number of sequenced bases = 98,964,033 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,379 duplication rate = 2.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8426 >>>>>>> ACTG content number of A's = 27,860,316 bp (28.15%) number of C's = 18,197,499 bp (18.39%) number of T's = 31,311,898 bp (31.64%) number of G's = 21,572,966 bp (21.8%) number of N's = 21,354 bp (0.02%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 810,583 number of insertions = 7,747 mapped reads with insertion percentage = 0.52% number of deletions = 24,701 mapped reads with deletion percentage = 1.65% homopolymer indels = 45.98% >>>>>>> Coverage mean coverageData = 0.032X std coverageData = 0.3682X There is a 2.84% of reference with a coverageData >= 1X There is a 0.25% 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% 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 10230055 0.04104324779194833 0.7824003706438444 chr2 243199373 12200232 0.050165556964655494 0.4188269335584344 chr3 198022430 4880789 0.024647657338615632 0.17264145900703018 chr4 191154276 4439991 0.023227264871647443 0.1898843786841453 chr5 180915260 2359607 0.013042609009322928 0.12722636464451273 chr6 171115067 7100268 0.041494113431869796 0.30447875770153937 chr7 159138663 4117589 0.025874221401495624 0.462297668719308 chr8 146364022 7042996 0.048119721662199195 0.3577892872320032 chr9 141213431 6170137 0.04369369794577118 0.3454388621189857 chr10 135534747 2105616 0.015535617593324611 0.3579328198225804 chr11 135006516 3865981 0.028635514155479724 0.2488999410811292 chr12 133851895 5317113 0.03972385299438607 0.22333456834136436 chr13 115169878 1293662 0.011232641923958625 0.11440275742943405 chr14 107349540 4182364 0.03896024146912972 0.23663430757335913 chr15 102531392 1788747 0.01744584721916191 0.1426459596802832 chr16 90354753 3862464 0.042747767790367375 0.259040182622184 chr17 81195210 4636233 0.05709983384487829 0.2936007905452032 chr18 78077248 2781867 0.035629675369705655 0.6511287809020769 chr19 59128983 2113064 0.03573651858683245 0.6040782277815476 chr20 63025520 1338254 0.021233525721009523 0.16234795946389433 chr21 48129895 1000848 0.020794726437695324 0.18406876427284427 chr22 51304566 1489123 0.029025155382856178 0.18516474773562686 chrMT 16571 32040 1.9334982801279343 1.7581759159550414 chrX 155270560 4459371 0.028720003328383693 0.21174560076213222 chrY 59373566 198555 0.0033441649773907805 0.11513505022642248