BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506320.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 14,912,300 number of mapped reads = 10,348,438 (69.4%) number of supplementary alignments = 172,789 (1.16%) number of secondary alignments = 0 number of mapped bases = 823,774,355 bp number of sequenced bases = 823,432,435 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,572,957 duplication rate = 14.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6261 >>>>>>> ACTG content number of A's = 222,206,650 bp (26.99%) number of C's = 158,239,366 bp (19.22%) number of T's = 239,339,353 bp (29.07%) number of G's = 203,452,431 bp (24.71%) number of N's = 194,635 bp (0.02%) GC percentage = 43.92% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 5,699,711 number of insertions = 65,413 mapped reads with insertion percentage = 0.62% number of deletions = 167,509 mapped reads with deletion percentage = 1.59% homopolymer indels = 42.91% >>>>>>> Coverage mean coverageData = 0.2661X std coverageData = 1.817X There is a 10.86% of reference with a coverageData >= 1X There is a 5.62% of reference with a coverageData >= 2X There is a 3.28% of reference with a coverageData >= 3X There is a 2.03% of reference with a coverageData >= 4X There is a 1.3% of reference with a coverageData >= 5X There is a 0.86% of reference with a coverageData >= 6X There is a 0.58% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 64513226 0.25882874731132566 3.3189250193239106 chr2 243199373 65008144 0.2673039128271108 1.929918171139288 chr3 198022430 50590708 0.2554796848013632 1.0459482860489535 chr4 191154276 49714109 0.26007322483332784 1.5283881952787928 chr5 180915260 59821641 0.33066111172711465 1.2103365496799523 chr6 171115067 32131941 0.18777972953135683 0.9948638222771675 chr7 159138663 40824349 0.25653319080605824 2.087320267516829 chr8 146364022 50861612 0.34750078130539486 2.322100223352588 chr9 141213431 24479079 0.17334809321359806 1.7470563385430813 chr10 135534747 46574752 0.3436369863146607 2.241786048487354 chr11 135006516 39351667 0.2914797608731715 1.7190079130090667 chr12 133851895 33369866 0.24930439722201916 1.0771998382338654 chr13 115169878 15183784 0.13183815302817287 0.7252071383276901 chr14 107349540 24229326 0.22570498206140427 1.1363951427560193 chr15 102531392 27706123 0.27022088025489793 1.0985785406187412 chr16 90354753 27159637 0.30058891312557734 1.4253454864330235 chr17 81195210 22121199 0.272444630662326 1.3795183034669651 chr18 78077248 15487260 0.1983581695912233 2.595768732698065 chr19 59128983 22278900 0.37678476560302077 2.460273901119723 chr20 63025520 20124360 0.3193049418711658 1.3069467390258502 chr21 48129895 12249310 0.25450523006543024 1.3730225575055894 chr22 51304566 8865719 0.17280565242477638 0.9888583930869186 chrMT 16571 261291 15.767968137106994 10.627363114633836 chrX 155270560 67950692 0.4376276610324584 1.5831882769712577 chrY 59373566 2915660 0.04910703864409963 1.4062414564839962