BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6003987.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 = 3,108,228 number of mapped reads = 2,364,076 (76.06%) number of supplementary alignments = 14,112 (0.45%) number of secondary alignments = 0 number of mapped bases = 152,736,479 bp number of sequenced bases = 152,659,174 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 323,919 duplication rate = 10.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7328 >>>>>>> ACTG content number of A's = 41,253,261 bp (27.02%) number of C's = 26,605,768 bp (17.43%) number of T's = 51,184,834 bp (33.53%) number of G's = 33,600,320 bp (22.01%) number of N's = 14,991 bp (0.01%) GC percentage = 39.44% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,580,508 number of insertions = 13,954 mapped reads with insertion percentage = 0.59% number of deletions = 46,549 mapped reads with deletion percentage = 1.95% homopolymer indels = 49.31% >>>>>>> Coverage mean coverageData = 0.0493X std coverageData = 0.5577X There is a 2.77% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% 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 15221938 0.061070812738316105 0.9506858585563726 chr2 243199373 14399628 0.059209149359114505 0.6677460049158362 chr3 198022430 11004740 0.055573199460283364 0.38988721458376624 chr4 191154276 8437627 0.044140404162342675 0.34642844215355584 chr5 180915260 9183552 0.05076162176700849 0.36883693787016353 chr6 171115067 10517663 0.06146544067916591 0.4593865378944731 chr7 159138663 7955708 0.04999230136802142 0.5006773157623421 chr8 146364022 9233247 0.06308413006032315 0.7635964396908099 chr9 141213431 5390373 0.038171815257431144 0.48919085600287754 chr10 135534747 7001707 0.051659866971235056 0.45853860927617324 chr11 135006516 5913413 0.04380094513364081 0.4571973513833524 chr12 133851895 5910240 0.04415507154381341 0.34673431775386504 chr13 115169878 3009533 0.026131251089803187 0.264206438544309 chr14 107349540 3387524 0.03155601784600102 0.31710646002993753 chr15 102531392 4262507 0.04157270194868709 0.33276622616215673 chr16 90354753 4737549 0.05243275912668369 0.39607161226421284 chr17 81195210 3098358 0.03815936925343256 0.346278679599055 chr18 78077248 4834816 0.061923494024789395 1.0068668232069335 chr19 59128983 2542134 0.04299302763248947 0.6255873650567128 chr20 63025520 3087096 0.048981682340740705 0.36525840258772474 chr21 48129895 3026723 0.06288654899413348 0.42964411419188764 chr22 51304566 1798455 0.035054482285260924 0.2919309273511075 chrMT 16571 1015659 61.2913523625611 33.47661944885458 chrX 155270560 7369137 0.0474599756708548 0.38693777989531347 chrY 59373566 397152 0.00668903734028709 0.14253601514315992