BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004141.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 = 2,160,015 number of mapped reads = 1,635,586 (75.72%) number of supplementary alignments = 22,931 (1.06%) number of secondary alignments = 0 number of mapped bases = 104,630,225 bp number of sequenced bases = 104,564,704 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 215,917 duplication rate = 10.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.935 >>>>>>> ACTG content number of A's = 29,476,155 bp (28.19%) number of C's = 18,135,543 bp (17.34%) number of T's = 34,513,797 bp (33.01%) number of G's = 22,371,792 bp (21.4%) number of N's = 67,417 bp (0.06%) GC percentage = 38.74% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 1,060,003 number of insertions = 8,324 mapped reads with insertion percentage = 0.51% number of deletions = 38,921 mapped reads with deletion percentage = 2.35% homopolymer indels = 43.66% >>>>>>> Coverage mean coverageData = 0.0338X std coverageData = 0.4191X There is a 1.96% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 9602991 0.038527450649761874 0.6353541575303866 chr2 243199373 8970693 0.03688616828794209 0.4170015650470403 chr3 198022430 9024587 0.045573559520504826 0.33650303460088543 chr4 191154276 5579721 0.029189621685470433 0.29177193226136017 chr5 180915260 6963778 0.038491932631885224 0.31058726694648153 chr6 171115067 6168635 0.03604963086038473 0.31720415587219886 chr7 159138663 5444499 0.03421229572602354 0.4349819149739966 chr8 146364022 5477792 0.03742580946566226 0.9840906018945511 chr9 141213431 3375330 0.023902329800343142 0.2990570229709569 chr10 135534747 3882455 0.02864545871768219 0.334033891627615 chr11 135006516 3459774 0.025626718639269234 0.2675456467450613 chr12 133851895 3379153 0.025245462531554 0.2504302537584401 chr13 115169878 3930516 0.03412798613887565 0.29003389078872077 chr14 107349540 3596883 0.03350627305901823 0.2927898940535779 chr15 102531392 2962661 0.028895160225660448 0.26422948637785143 chr16 90354753 3474406 0.038452941152968455 0.3171376661455969 chr17 81195210 1807649 0.02226300048980722 0.23157104934261605 chr18 78077248 4048005 0.051846153696400776 0.5597453635323053 chr19 59128983 1374684 0.023248903164798218 0.4603528446161396 chr20 63025520 2581398 0.04095798019595872 0.3274223008739184 chr21 48129895 1650957 0.03430211098528264 0.3027045577509172 chr22 51304566 780529 0.01521363615082525 0.18227914391043543 chrMT 16571 29132 1.758010983042665 2.221871469280572 chrX 155270560 6690503 0.043089320989117316 0.34207167545323725 chrY 59373566 373494 0.006290577190529536 0.18609725109150205