BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238534.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 = 2,882,268 number of mapped reads = 2,585,097 (89.69%) number of supplementary alignments = 20,726 (0.72%) number of secondary alignments = 0 number of mapped bases = 163,243,065 bp number of sequenced bases = 163,176,998 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 923,135 duplication rate = 20.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9731 >>>>>>> ACTG content number of A's = 40,856,792 bp (25.04%) number of C's = 28,860,425 bp (17.69%) number of T's = 54,632,479 bp (33.48%) number of G's = 38,815,796 bp (23.79%) number of N's = 11,506 bp (0.01%) GC percentage = 41.47% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 898,362 number of insertions = 11,100 mapped reads with insertion percentage = 0.43% number of deletions = 38,984 mapped reads with deletion percentage = 1.5% homopolymer indels = 42.85% >>>>>>> Coverage mean coverageData = 0.0527X std coverageData = 0.8685X There is a 1.69% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.66% of reference with a coverageData >= 3X There is a 0.47% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 6074167 0.024369716615470337 1.0143008589483988 chr2 243199373 10336359 0.04250158572571649 1.710261986520029 chr3 198022430 11333205 0.05723192569649812 0.6134988071078015 chr4 191154276 6916957 0.036185206759382145 0.48168681390051593 chr5 180915260 13322082 0.07363713818281553 0.6920282745917354 chr6 171115067 8894660 0.05198057749058416 0.7599295446207383 chr7 159138663 15203600 0.09553680867609149 1.1740917118443646 chr8 146364022 9756768 0.06666097218891676 0.7540184106265797 chr9 141213431 2207336 0.015631204371771124 0.4051160839672234 chr10 135534747 7777715 0.057385395052974866 0.6492551734245399 chr11 135006516 7079870 0.05244095033161214 0.6631707890474229 chr12 133851895 3689267 0.027562306831741157 0.4140468402312525 chr13 115169878 7155055 0.06212609689488427 0.6907381396253637 chr14 107349540 5862988 0.054615865144834345 0.5946658864096455 chr15 102531392 5172834 0.05045122180726855 0.6472856443397453 chr16 90354753 3514423 0.03889582875623599 0.5332548384419237 chr17 81195210 4312314 0.0531104482641279 0.603464079622968 chr18 78077248 5068878 0.06492131997275313 1.5246484285647812 chr19 59128983 2776944 0.04696417660354483 0.8054183574902056 chr20 63025520 4741188 0.07522647968632389 0.7338824296690266 chr21 48129895 3075268 0.06389517367532176 0.6456894203512356 chr22 51304566 2372540 0.04624422707327843 0.5403720438674856 chrMT 16571 32092 1.9366362923179048 3.1553973014205745 chrX 155270560 16031826 0.10325090603138161 0.8462669627080834 chrY 59373566 534729 0.009006179618721234 0.2863683692495537