BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068957.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 = 2,459,804 number of mapped reads = 2,025,127 (82.33%) number of supplementary alignments = 11,365 (0.46%) number of secondary alignments = 0 number of mapped bases = 131,955,236 bp number of sequenced bases = 131,900,251 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,188 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.243 >>>>>>> ACTG content number of A's = 35,810,279 bp (27.15%) number of C's = 22,675,080 bp (17.19%) number of T's = 43,764,160 bp (33.18%) number of G's = 29,334,079 bp (22.24%) number of N's = 316,653 bp (0.24%) GC percentage = 39.43% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,271,188 number of insertions = 11,764 mapped reads with insertion percentage = 0.58% number of deletions = 33,533 mapped reads with deletion percentage = 1.64% homopolymer indels = 48.09% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.3806X There is a 3.62% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 7903632 0.03170957796731026 0.659610748006299 chr2 243199373 11306545 0.04649084765526924 0.428242184874606 chr3 198022430 8212007 0.04147008497976719 0.22931630739071418 chr4 191154276 4901198 0.025640012363626122 0.2141561452521631 chr5 180915260 5984787 0.03308060912053522 0.20742800477654458 chr6 171115067 13813498 0.0807263687656447 0.44397118784683215 chr7 159138663 8462045 0.053174036029195494 0.4546250716131822 chr8 146364022 8369563 0.0571831990241427 0.5417897940598866 chr9 141213431 5401565 0.038251071174667514 0.364535300680297 chr10 135534747 12179562 0.08986302235839198 0.4723408362848536 chr11 135006516 6474271 0.04795524832297724 0.3826097819634477 chr12 133851895 5656451 0.042259028159444434 0.234905531227543 chr13 115169878 2322444 0.020165376922601237 0.1590794225670441 chr14 107349540 3318720 0.030915083567195537 0.20870544862811594 chr15 102531392 3288638 0.032074449940170516 0.20077482642060138 chr16 90354753 2732787 0.030245082956510322 0.22548568916085274 chr17 81195210 2358897 0.02905216945679431 0.22456265902472503 chr18 78077248 4574673 0.05859162710243066 0.5866627436731379 chr19 59128983 2672442 0.04519681997574692 0.4589032033532114 chr20 63025520 1617582 0.02566550819414104 0.19371029967736322 chr21 48129895 1418060 0.029463184991365552 0.22848182365342753 chr22 51304566 1181042 0.023020212275063394 0.17199924178730855 chrMT 16571 120509 7.272282903868203 4.49370587776535 chrX 155270560 7326770 0.047187116475911464 0.28644494310358665 chrY 59373566 357548 0.006022006493596831 0.17173115267751088