BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124954.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,145,168 number of mapped reads = 6,070,454 (98.78%) number of supplementary alignments = 23,121 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,040,940 number of mapped paired reads (second in pair) = 3,029,514 number of mapped paired reads (both in pair) = 6,047,916 number of mapped paired reads (singletons) = 22,538 number of mapped bases = 527,853,145 bp number of sequenced bases = 527,587,617 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 450,909 duplication rate = 4.99% >>>>>>> Insert size mean insert size = 27,587.9883 std insert size = 1,549,498.5266 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.788 >>>>>>> ACTG content number of A's = 149,035,585 bp (28.25%) number of C's = 97,715,838 bp (18.52%) number of T's = 158,252,856 bp (30%) number of G's = 122,575,747 bp (23.23%) number of N's = 7,591 bp (0%) GC percentage = 41.75% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 3,784,207 number of insertions = 65,334 mapped reads with insertion percentage = 1.06% number of deletions = 166,116 mapped reads with deletion percentage = 2.69% homopolymer indels = 48.06% >>>>>>> Coverage mean coverageData = 0.1705X std coverageData = 1.5932X There is a 11.88% of reference with a coverageData >= 1X There is a 3.18% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 43188334 0.1732727237618397 1.8132625485451934 chr2 243199373 39299056 0.16159192976208867 1.5555541579026073 chr3 198022430 38085951 0.19233150002249746 0.5680450948557055 chr4 191154276 29086298 0.15216137775542096 0.8865315598677348 chr5 180915260 22309272 0.12331337887141196 0.44949366165496313 chr6 171115067 45368501 0.2651344606609072 2.4590555109878487 chr7 159138663 23488073 0.14759501278454248 1.8572344496807074 chr8 146364022 38032465 0.2598484551073624 0.9524461117042814 chr9 141213431 21610980 0.15303770928135016 1.924749987490716 chr10 135534747 28934447 0.21348360948355186 3.850497752860242 chr11 135006516 26216211 0.1941847829033674 1.90389237666645 chr12 133851895 24079901 0.17989958976673434 0.545379671895058 chr13 115169878 16419348 0.14256634013279063 0.4774940478645242 chr14 107349540 13190753 0.1228766606731617 0.5218289730745264 chr15 102531392 9373165 0.09141751435501821 0.39265862609594465 chr16 90354753 11859654 0.1312565593533303 1.5433130491716334 chr17 81195210 11851667 0.14596510065064183 2.065357619173716 chr18 78077248 18131316 0.23222278531128557 2.3425319221166516 chr19 59128983 8226195 0.13912289003854506 1.1695304632107888 chr20 63025520 13639624 0.21641430328539932 0.6393548091174038 chr21 48129895 6523773 0.1355451326041746 0.5803361092500554 chr22 51304566 4317582 0.08415590144549707 0.3714847050421027 chrMT 16571 77322 4.666103433709493 3.683622885568539 chrX 155270560 33483249 0.21564454330556931 1.085874087093596 chrY 59373566 1060008 0.017853197498698327 0.8072480807214898