BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124788.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 = 679,163 number of mapped reads = 677,878 (99.81%) number of supplementary alignments = 319,494 (47.04%) number of secondary alignments = 0 number of mapped bases = 101,011,484 bp number of sequenced bases = 100,977,162 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 984,002 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.1921 >>>>>>> ACTG content number of A's = 28,136,871 bp (27.86%) number of C's = 17,307,876 bp (17.14%) number of T's = 34,353,774 bp (34.02%) number of G's = 21,178,641 bp (20.97%) number of N's = 0 bp (0%) GC percentage = 38.11% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 789,525 number of insertions = 7,140 mapped reads with insertion percentage = 1.05% number of deletions = 32,801 mapped reads with deletion percentage = 4.79% homopolymer indels = 53.57% >>>>>>> Coverage mean coverageData = 0.0326X std coverageData = 100.7518X There is a 0.05% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 1193870 0.004789837614888028 3.097663211774511 chr2 243199373 140935 5.79503961138913E-4 0.027146359261240777 chr3 198022430 102129 5.157446052954708E-4 0.02415975310419505 chr4 191154276 97186 5.08416562965089E-4 0.027275784392335023 chr5 180915260 88757 4.905998532130457E-4 0.022926743702159063 chr6 171115067 90437 5.285157034126048E-4 0.08791253441398388 chr7 159138663 99977 6.282382804736772E-4 0.02526622460584169 chr8 146364022 911795 0.006229638865758964 3.846002905309069 chr9 141213431 79280 5.614196853555665E-4 0.09577728649795936 chr10 135534747 97592233 0.7200532347620053 481.47594692065985 chr11 135006516 66492 4.925095615384964E-4 0.030315545236324883 chr12 133851895 73135 5.463874829713842E-4 0.023520241406268388 chr13 115169878 41276 3.5839232199238763E-4 0.019122514744576217 chr14 107349540 55863 5.203841581435748E-4 0.023793125434691552 chr15 102531392 46024 4.4887715949472334E-4 0.021623087625250153 chr16 90354753 56605 6.264750676702088E-4 0.02713454466160233 chr17 81195210 44761 5.512763622386099E-4 0.02593844445890786 chr18 78077248 28751 3.6823787641695566E-4 0.019736837912888532 chr19 59128983 31152 5.268482294038441E-4 0.023220052930837187 chr20 63025520 35449 5.624547008894175E-4 0.024016985666177795 chr21 48129895 19019 3.9515980660252844E-4 0.02018228988196415 chr22 51304566 16092 3.1365629328196636E-4 0.01796709852597966 chrMT 16571 761 0.04592360147245187 0.2270219416678486 chrX 155270560 62195 4.0055886962731376E-4 0.02050371598258566 chrY 59373566 37310 6.283941240787188E-4 0.03034206656038039