BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504609.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 = 434,871,932 number of mapped reads = 289,771,002 (66.63%) number of supplementary alignments = 1,831,032 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 145,061,853 number of mapped paired reads (second in pair) = 144,709,149 number of mapped paired reads (both in pair) = 288,156,098 number of mapped paired reads (singletons) = 1,614,904 number of mapped bases = 28,779,464,138 bp number of sequenced bases = 28,772,154,630 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,779,805 duplication rate = 22.48% >>>>>>> Insert size mean insert size = 24,279.4753 std insert size = 1,506,321.3125 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.7843 >>>>>>> ACTG content number of A's = 7,429,398,026 bp (25.82%) number of C's = 6,893,439,253 bp (23.96%) number of T's = 7,478,871,126 bp (25.99%) number of G's = 6,964,954,146 bp (24.21%) number of N's = 5,492,079 bp (0.02%) GC percentage = 48.17% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 140,340,491 number of insertions = 2,138,659 mapped reads with insertion percentage = 0.72% number of deletions = 2,817,301 mapped reads with deletion percentage = 0.94% homopolymer indels = 39.95% >>>>>>> Coverage mean coverageData = 9.2966X std coverageData = 23.89X There is a 67.97% of reference with a coverageData >= 1X There is a 58.03% of reference with a coverageData >= 2X There is a 50.52% of reference with a coverageData >= 3X There is a 44.72% of reference with a coverageData >= 4X There is a 39.95% of reference with a coverageData >= 5X There is a 35.97% of reference with a coverageData >= 6X There is a 32.6% of reference with a coverageData >= 7X There is a 29.69% of reference with a coverageData >= 8X There is a 27.17% of reference with a coverageData >= 9X There is a 24.96% of reference with a coverageData >= 10X There is a 23.01% of reference with a coverageData >= 11X There is a 21.29% of reference with a coverageData >= 12X There is a 19.75% of reference with a coverageData >= 13X There is a 18.37% of reference with a coverageData >= 14X There is a 17.13% of reference with a coverageData >= 15X There is a 16.01% of reference with a coverageData >= 16X There is a 15% of reference with a coverageData >= 17X There is a 14.08% of reference with a coverageData >= 18X There is a 13.23% of reference with a coverageData >= 19X There is a 12.46% of reference with a coverageData >= 20X There is a 11.76% of reference with a coverageData >= 21X There is a 11.11% of reference with a coverageData >= 22X There is a 10.51% of reference with a coverageData >= 23X There is a 9.95% of reference with a coverageData >= 24X There is a 9.44% of reference with a coverageData >= 25X There is a 8.97% of reference with a coverageData >= 26X There is a 8.53% of reference with a coverageData >= 27X There is a 8.12% of reference with a coverageData >= 28X There is a 7.73% of reference with a coverageData >= 29X There is a 7.38% of reference with a coverageData >= 30X There is a 7.04% of reference with a coverageData >= 31X There is a 6.73% of reference with a coverageData >= 32X There is a 6.44% of reference with a coverageData >= 33X There is a 6.16% of reference with a coverageData >= 34X There is a 5.9% of reference with a coverageData >= 35X There is a 5.66% of reference with a coverageData >= 36X There is a 5.43% of reference with a coverageData >= 37X There is a 5.22% of reference with a coverageData >= 38X There is a 5.01% of reference with a coverageData >= 39X There is a 4.82% of reference with a coverageData >= 40X There is a 4.64% of reference with a coverageData >= 41X There is a 4.46% of reference with a coverageData >= 42X There is a 4.3% of reference with a coverageData >= 43X There is a 4.15% of reference with a coverageData >= 44X There is a 4% of reference with a coverageData >= 45X There is a 3.86% of reference with a coverageData >= 46X There is a 3.72% of reference with a coverageData >= 47X There is a 3.6% of reference with a coverageData >= 48X There is a 3.48% of reference with a coverageData >= 49X There is a 3.36% of reference with a coverageData >= 50X There is a 3.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2916280186 11.700192257494917 23.298463513522538 chr2 243199373 1284790927 5.28287105000061 13.281238702015957 chr3 198022430 1626467511 8.213551924395635 22.27270232332073 chr4 191154276 970871084 5.078992237662526 9.640432013670983 chr5 180915260 1402767605 7.753727380432142 22.14055709422709 chr6 171115067 1220555323 7.132950618544888 13.834124864470331 chr7 159138663 2303051143 14.471977454026995 26.737157975137315 chr8 146364022 2594174010 17.724123555445885 42.25880595876847 chr9 141213431 878439176 6.220648912637778 17.375510926623274 chr10 135534747 1414383415 10.435577933384124 21.58522653445702 chr11 135006516 1621928999 12.013709019792794 27.587794645504214 chr12 133851895 868432633 6.4880114921047625 16.032388100377787 chr13 115169878 786998215 6.833368487201141 15.236670904414042 chr14 107349540 1019839272 9.500173657008684 19.026307249114925 chr15 102531392 877926037 8.562509684838766 17.842424120290172 chr16 90354753 1073642103 11.882519373385925 26.812854644257744 chr17 81195210 1397607290 17.212927831580213 55.40312431857044 chr18 78077248 657696891 8.423668966918505 24.23173048641761 chr19 59128983 604445123 10.222484682342667 21.915495693833083 chr20 63025520 1633305793 25.914991149616853 46.23711686973498 chr21 48129895 239724287 4.980777269512015 12.906709325986428 chr22 51304566 316172915 6.162666204017786 15.886570249272468 chrMT 16571 481899 29.080864160280008 12.641264819454225 chrX 155270560 1041865210 6.709998405364159 12.550589045165317 chrY 59373566 27617091 0.465141187578324 10.707586946577184