BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975260.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 141,845,710 number of mapped reads = 140,818,675 (99.28%) number of supplementary alignments = 300,517 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 70,371,046 number of mapped paired reads (second in pair) = 70,447,629 number of mapped paired reads (both in pair) = 140,475,850 number of mapped paired reads (singletons) = 342,825 number of mapped bases = 12,813,814,811 bp number of sequenced bases = 12,809,245,552 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,123,641 duplication rate = 45.23% >>>>>>> Insert size mean insert size = 108,706.893 std insert size = 3,264,572.7542 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 55.5721 >>>>>>> ACTG content number of A's = 3,399,700,494 bp (26.54%) number of C's = 2,771,818,518 bp (21.64%) number of T's = 3,525,595,557 bp (27.52%) number of G's = 3,111,799,117 bp (24.29%) number of N's = 331,866 bp (0%) GC percentage = 45.93% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 79,603,162 number of insertions = 1,141,050 mapped reads with insertion percentage = 0.8% number of deletions = 3,052,749 mapped reads with deletion percentage = 2.13% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 4.1392X std coverageData = 52.5502X There is a 29.14% of reference with a coverageData >= 1X There is a 18.01% of reference with a coverageData >= 2X There is a 11.7% of reference with a coverageData >= 3X There is a 8.46% of reference with a coverageData >= 4X There is a 6.34% of reference with a coverageData >= 5X There is a 5.06% of reference with a coverageData >= 6X There is a 4.17% of reference with a coverageData >= 7X There is a 3.57% of reference with a coverageData >= 8X There is a 3.14% of reference with a coverageData >= 9X There is a 2.82% of reference with a coverageData >= 10X There is a 2.58% of reference with a coverageData >= 11X There is a 2.4% of reference with a coverageData >= 12X There is a 2.26% of reference with a coverageData >= 13X There is a 2.14% of reference with a coverageData >= 14X There is a 2.05% of reference with a coverageData >= 15X There is a 1.97% of reference with a coverageData >= 16X There is a 1.9% of reference with a coverageData >= 17X There is a 1.84% of reference with a coverageData >= 18X There is a 1.79% of reference with a coverageData >= 19X There is a 1.74% of reference with a coverageData >= 20X There is a 1.7% of reference with a coverageData >= 21X There is a 1.66% of reference with a coverageData >= 22X There is a 1.63% of reference with a coverageData >= 23X There is a 1.6% of reference with a coverageData >= 24X There is a 1.57% of reference with a coverageData >= 25X There is a 1.54% of reference with a coverageData >= 26X There is a 1.51% of reference with a coverageData >= 27X There is a 1.49% of reference with a coverageData >= 28X There is a 1.46% of reference with a coverageData >= 29X There is a 1.44% of reference with a coverageData >= 30X There is a 1.42% of reference with a coverageData >= 31X There is a 1.4% of reference with a coverageData >= 32X There is a 1.38% of reference with a coverageData >= 33X There is a 1.36% of reference with a coverageData >= 34X There is a 1.34% of reference with a coverageData >= 35X There is a 1.32% of reference with a coverageData >= 36X There is a 1.31% of reference with a coverageData >= 37X There is a 1.29% of reference with a coverageData >= 38X There is a 1.27% of reference with a coverageData >= 39X There is a 1.26% of reference with a coverageData >= 40X There is a 1.24% of reference with a coverageData >= 41X There is a 1.23% of reference with a coverageData >= 42X There is a 1.22% of reference with a coverageData >= 43X There is a 1.2% of reference with a coverageData >= 44X There is a 1.19% of reference with a coverageData >= 45X There is a 1.18% of reference with a coverageData >= 46X There is a 1.16% of reference with a coverageData >= 47X There is a 1.15% of reference with a coverageData >= 48X There is a 1.14% of reference with a coverageData >= 49X There is a 1.13% of reference with a coverageData >= 50X There is a 1.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1318074249 5.288148305155075 60.59790164526893 chr2 243199373 1034610396 4.254165556586365 51.84061982429823 chr3 198022430 852628120 4.3057148627052 54.00442844669197 chr4 191154276 582900356 3.049371262822287 41.656788333356566 chr5 180915260 658437706 3.639481301908971 48.741580961530424 chr6 171115067 758888023 4.434957343645256 55.39807225569505 chr7 159138663 608542867 3.823978758700518 50.93474170279527 chr8 146364022 440005552 3.0062411922514674 39.09885304811862 chr9 141213431 514089633 3.6405151362691557 47.898519325160464 chr10 135534747 592279985 4.3699493901737245 56.713694669976675 chr11 135006516 739662315 5.47871567176802 63.61402213595446 chr12 133851895 734518886 5.487549399281945 61.51732913446361 chr13 115169878 272926927 2.3697769915150904 36.14743449448291 chr14 107349540 417518914 3.8893405039276367 49.481884013405875 chr15 102531392 448793910 4.377136613926006 55.14922959029239 chr16 90354753 411861971 4.558276762706662 53.85613084169297 chr17 81195210 582332775 7.172008976884228 72.9522807225816 chr18 78077248 243702156 3.121295412461259 44.382869983166394 chr19 59128983 482261475 8.156092841982417 78.54318085560399 chr20 63025520 313845312 4.9796544637791165 64.40050845823558 chr21 48129895 129823022 2.6973468776526524 41.103247231467314 chr22 51304566 214699358 4.184800198875086 51.741785005746856 chrMT 16571 774881 46.76126968800917 51.536034539786534 chrX 155270560 438335773 2.823044967442637 39.10229344610856 chrY 59373566 22300249 0.3755922121975965 10.150467559207451