BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068101.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 = 2,415,681 number of mapped reads = 2,073,936 (85.85%) number of supplementary alignments = 19,529 (0.81%) number of secondary alignments = 0 number of mapped bases = 132,990,095 bp number of sequenced bases = 132,937,009 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 210,556 duplication rate = 8.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6209 >>>>>>> ACTG content number of A's = 35,024,440 bp (26.35%) number of C's = 24,034,425 bp (18.08%) number of T's = 42,745,650 bp (32.15%) number of G's = 31,130,082 bp (23.42%) number of N's = 2,412 bp (0%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 990,182 number of insertions = 9,180 mapped reads with insertion percentage = 0.44% number of deletions = 33,352 mapped reads with deletion percentage = 1.59% homopolymer indels = 46.24% >>>>>>> Coverage mean coverageData = 0.043X std coverageData = 0.4018X There is a 2.87% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% 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% 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 11949628 0.047942219570237296 0.4146713190000749 chr2 243199373 7415166 0.030490070383528498 0.6691059350223308 chr3 198022430 15289693 0.07721192493193826 0.3921761877192184 chr4 191154276 5415085 0.028328348773113503 0.2399849292314988 chr5 180915260 7087220 0.03917425207801708 0.2755932552153503 chr6 171115067 10042118 0.05868634583768126 0.42629280343974074 chr7 159138663 21966439 0.1380333263199528 0.8944600864240593 chr8 146364022 2508756 0.01714052378254541 0.24294183069735376 chr9 141213431 5967650 0.0422597904302743 0.3346875902483702 chr10 135534747 12576822 0.09279407884975799 0.4458017354737793 chr11 135006516 2496084 0.01848861872711388 0.21061371388750655 chr12 133851895 3704484 0.02767599218524325 0.23484687465824755 chr13 115169878 3791621 0.03292198503501063 0.2591650476873816 chr14 107349540 2287831 0.02131197767591738 0.20900930667847356 chr15 102531392 1213905 0.011839349650105208 0.15787002721862525 chr16 90354753 3291678 0.03643060149807504 0.27793479378464103 chr17 81195210 1949870 0.02401459396434839 0.21344310254025742 chr18 78077248 2358443 0.030206533406505313 0.3859984674191254 chr19 59128983 1938719 0.032787964575680256 0.3631068434142269 chr20 63025520 2772611 0.04399187821060421 0.3033726947946393 chr21 48129895 2304671 0.047884397005229284 0.3085454547066809 chr22 51304566 1459760 0.028452828155685013 0.23750207807091742 chrMT 16571 119789 7.228833504314767 5.580946840477256 chrX 155270560 2905052 0.018709612433934673 0.20999401810248777 chrY 59373566 177000 0.0029811246304458114 0.07867821954623991