BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046483.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 7,330,850 number of mapped reads = 7,295,937 (99.52%) number of supplementary alignments = 31,330 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,653,161 number of mapped paired reads (second in pair) = 3,642,776 number of mapped paired reads (both in pair) = 7,275,952 number of mapped paired reads (singletons) = 19,985 number of mapped bases = 660,672,342 bp number of sequenced bases = 660,492,910 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,020,291 duplication rate = 47.29% >>>>>>> Insert size mean insert size = 19,265.0898 std insert size = 1,286,987.9735 median insert size = 103 >>>>>>> Mapping quality mean mapping quality = 52.7967 >>>>>>> ACTG content number of A's = 192,211,969 bp (29.1%) number of C's = 138,809,313 bp (21.02%) number of T's = 186,205,304 bp (28.19%) number of G's = 143,216,647 bp (21.68%) number of N's = 49,677 bp (0.01%) GC percentage = 42.7% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 2,996,611 number of insertions = 52,320 mapped reads with insertion percentage = 0.71% number of deletions = 64,771 mapped reads with deletion percentage = 0.86% homopolymer indels = 46.24% >>>>>>> Coverage mean coverageData = 0.2134X std coverageData = 13.4001X There is a 2.38% of reference with a coverageData >= 1X There is a 1.67% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 129209687 0.5183926382273687 26.966306212113903 chr2 243199373 53831232 0.22134609697369573 14.79711223635073 chr3 198022430 36538491 0.18451693073355377 9.663885913843549 chr4 191154276 22793070 0.11923913227031344 7.695991128528007 chr5 180915260 37205696 0.20565261327319762 11.53020165494954 chr6 171115067 48091703 0.28104890962056545 12.323166682452658 chr7 159138663 49425156 0.31057918338801177 14.962138987632034 chr8 146364022 43300867 0.2958436534355417 15.006425437155539 chr9 141213431 11546701 0.08176772505442488 4.262710352833364 chr10 135534747 24560785 0.18121393623142262 11.556265495712777 chr11 135006516 18559642 0.13747219430505117 6.846221414500295 chr12 133851895 17039037 0.12729768973386593 6.278783363886876 chr13 115169878 19434500 0.1687463800213455 10.362230455056233 chr14 107349540 22890455 0.21323291185039078 11.28474577002914 chr15 102531392 16123520 0.15725447285451855 9.110985402829936 chr16 90354753 35079418 0.38824098163380516 24.480127012303967 chr17 81195210 27326816 0.3365569964040982 15.532088597793521 chr18 78077248 4277792 0.054789226177643965 3.003652612744928 chr19 59128983 3881351 0.0656421065114548 1.7308848000323946 chr20 63025520 14992340 0.23787729161139806 15.531804006155308 chr21 48129895 4647336 0.0965581994309358 10.078087940295706 chr22 51304566 4547606 0.08863940102329293 4.371421077277097 chrMT 16571 45533 2.7477520970369924 2.5672664325117465 chrX 155270560 15144044 0.09753326065160066 8.172855378524178 chrY 59373566 179564 0.003024308831307185 0.14951780782024782