BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240037.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 = 2,046,070 number of mapped reads = 1,652,192 (80.75%) number of supplementary alignments = 5,646 (0.28%) number of secondary alignments = 0 number of mapped bases = 100,661,963 bp number of sequenced bases = 100,605,693 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,446 duplication rate = 5.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1447 >>>>>>> ACTG content number of A's = 26,528,997 bp (26.37%) number of C's = 16,910,159 bp (16.81%) number of T's = 32,699,573 bp (32.5%) number of G's = 24,403,403 bp (24.26%) number of N's = 63,561 bp (0.06%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 1,003,797 number of insertions = 7,347 mapped reads with insertion percentage = 0.44% number of deletions = 32,972 mapped reads with deletion percentage = 1.97% homopolymer indels = 49.8% >>>>>>> Coverage mean coverageData = 0.0325X std coverageData = 0.3134X There is a 2.62% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 7699669 0.030891273085333657 0.4420566859206908 chr2 243199373 11099445 0.04563928295982901 0.3923103777432513 chr3 198022430 7067218 0.035688977253738374 0.23246871594075316 chr4 191154276 6466521 0.03382880642439827 0.2310242737581796 chr5 180915260 5400715 0.029852180518105547 0.2130075812150053 chr6 171115067 5908615 0.03453006858829094 0.27089934268489807 chr7 159138663 6037590 0.03793917760890073 0.5907687736321873 chr8 146364022 5849063 0.039962436943690983 0.3711466156983541 chr9 141213431 3794990 0.026874143437531802 0.2952815300261231 chr10 135534747 4250972 0.031364444130330654 0.263246651025288 chr11 135006516 4325963 0.032042623779729267 0.27786251395001715 chr12 133851895 4508271 0.033681039779078215 0.2260008684790436 chr13 115169878 2463986 0.021394361466632796 0.17641660909390708 chr14 107349540 3329924 0.031019452901242056 0.23008381543255338 chr15 102531392 2609736 0.02545304368831743 0.2168855016260602 chr16 90354753 2874191 0.03181006980341145 0.22431517365644585 chr17 81195210 2556867 0.031490367473647765 0.23006098089264512 chr18 78077248 2384515 0.030540459110444056 0.4269982849989337 chr19 59128983 1738688 0.029405004310660985 0.3202116803604834 chr20 63025520 2043066 0.032416487797324006 0.22612256654332646 chr21 48129895 1455825 0.030247832454236602 0.22053004929941178 chr22 51304566 956338 0.01864040717155662 0.16177026155746324 chrMT 16571 46558 2.809607145012371 3.7284479116530984 chrX 155270560 5558698 0.03580007697531329 0.25933917734385176 chrY 59373566 234539 0.00395022593050921 0.08558064637255368