BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124808.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 = 734,442 number of mapped reads = 732,423 (99.73%) number of supplementary alignments = 354,323 (48.24%) number of secondary alignments = 0 number of mapped bases = 109,339,669 bp number of sequenced bases = 109,306,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,076,513 duplication rate = 5.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.6156 >>>>>>> ACTG content number of A's = 30,722,895 bp (28.11%) number of C's = 18,837,782 bp (17.23%) number of T's = 37,247,229 bp (34.08%) number of G's = 22,498,905 bp (20.58%) number of N's = 0 bp (0%) GC percentage = 37.82% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 832,077 number of insertions = 7,556 mapped reads with insertion percentage = 1.03% number of deletions = 31,688 mapped reads with deletion percentage = 4.28% homopolymer indels = 51.51% >>>>>>> Coverage mean coverageData = 0.0353X std coverageData = 105.5707X There is a 0.04% 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 2598915 0.010426914844075754 8.965101376373864 chr2 243199373 138479 5.694052508926493E-4 0.14226976999210814 chr3 198022430 85457 4.3155212265600415E-4 0.025942347214583578 chr4 191154276 74060 3.8743574849458244E-4 0.02181189909101481 chr5 180915260 76191 4.211419202559253E-4 0.026918675801298798 chr6 171115067 69021 4.033601553041498E-4 0.033097952849633815 chr7 159138663 66125 4.155181321336098E-4 0.022726558957587743 chr8 146364022 1115592 0.007622037060446453 3.590885692281245 chr9 141213431 52627 3.72677015403726E-4 0.026291314246049358 chr10 135534747 104408102 0.7703419551888049 504.3800158662488 chr11 135006516 52409 3.8819607788412227E-4 0.026215092580767006 chr12 133851895 52266 3.904763544811973E-4 0.019893043327233014 chr13 115169878 37670 3.2708205178440844E-4 0.0185940518395834 chr14 107349540 36654 3.414453382846354E-4 0.02109567481110565 chr15 102531392 181906 0.0017741493258962094 0.8372107526318976 chr16 90354753 38138 4.2209179632199314E-4 0.02110815253520492 chr17 81195210 33560 4.1332487470627883E-4 0.023451496914819424 chr18 78077248 30226 3.8712942341410396E-4 0.020592372050186217 chr19 59128983 65391 0.0011059043582738435 0.32126919761954326 chr20 63025520 26658 4.2297152010804513E-4 0.020618184036570536 chr21 48129895 16223 3.370670141707145E-4 0.018561159211674155 chr22 51304566 17514 3.4137312456750926E-4 0.02677017645231184 chrMT 16571 296 0.017862530927523986 0.13245173051488318 chrX 155270560 46418 2.9894913755704883E-4 0.07136508495408878 chrY 59373566 19771 3.329933054720008E-4 0.02141916881902206