BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163157.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 = 84,207,346 number of mapped reads = 81,901,699 (97.26%) number of supplementary alignments = 391,154 (0.46%) number of secondary alignments = 0 number of mapped bases = 7,985,464,133 bp number of sequenced bases = 7,984,590,598 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,466,432 duplication rate = 43.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.182 >>>>>>> ACTG content number of A's = 1,945,391,811 bp (24.36%) number of C's = 2,040,713,923 bp (25.56%) number of T's = 1,938,694,088 bp (24.28%) number of G's = 2,046,553,880 bp (25.63%) number of N's = 13,236,896 bp (0.17%) GC percentage = 51.19% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 51,069,747 number of insertions = 529,278 mapped reads with insertion percentage = 0.64% number of deletions = 372,637 mapped reads with deletion percentage = 0.45% homopolymer indels = 43.59% >>>>>>> Coverage mean coverageData = 2.5795X std coverageData = 32.8959X There is a 9.68% of reference with a coverageData >= 1X There is a 6.4% of reference with a coverageData >= 2X There is a 4.68% of reference with a coverageData >= 3X There is a 4.16% of reference with a coverageData >= 4X There is a 3.76% of reference with a coverageData >= 5X There is a 3.51% of reference with a coverageData >= 6X There is a 3.31% of reference with a coverageData >= 7X There is a 3.14% of reference with a coverageData >= 8X There is a 3% of reference with a coverageData >= 9X There is a 2.88% of reference with a coverageData >= 10X There is a 2.77% of reference with a coverageData >= 11X There is a 2.67% of reference with a coverageData >= 12X There is a 2.58% of reference with a coverageData >= 13X There is a 2.49% of reference with a coverageData >= 14X There is a 2.42% of reference with a coverageData >= 15X There is a 2.34% of reference with a coverageData >= 16X There is a 2.28% of reference with a coverageData >= 17X There is a 2.21% of reference with a coverageData >= 18X There is a 2.15% of reference with a coverageData >= 19X There is a 2.1% of reference with a coverageData >= 20X There is a 2.05% of reference with a coverageData >= 21X There is a 2% of reference with a coverageData >= 22X There is a 1.95% of reference with a coverageData >= 23X There is a 1.9% of reference with a coverageData >= 24X There is a 1.86% of reference with a coverageData >= 25X There is a 1.82% of reference with a coverageData >= 26X There is a 1.78% of reference with a coverageData >= 27X There is a 1.74% of reference with a coverageData >= 28X There is a 1.7% of reference with a coverageData >= 29X There is a 1.67% of reference with a coverageData >= 30X There is a 1.63% of reference with a coverageData >= 31X There is a 1.6% of reference with a coverageData >= 32X There is a 1.57% of reference with a coverageData >= 33X There is a 1.54% of reference with a coverageData >= 34X There is a 1.51% of reference with a coverageData >= 35X There is a 1.48% of reference with a coverageData >= 36X There is a 1.46% of reference with a coverageData >= 37X There is a 1.43% of reference with a coverageData >= 38X There is a 1.4% of reference with a coverageData >= 39X There is a 1.38% of reference with a coverageData >= 40X There is a 1.35% of reference with a coverageData >= 41X There is a 1.33% of reference with a coverageData >= 42X There is a 1.31% of reference with a coverageData >= 43X There is a 1.29% of reference with a coverageData >= 44X There is a 1.26% of reference with a coverageData >= 45X There is a 1.24% of reference with a coverageData >= 46X There is a 1.22% of reference with a coverageData >= 47X There is a 1.2% of reference with a coverageData >= 48X There is a 1.18% of reference with a coverageData >= 49X There is a 1.17% of reference with a coverageData >= 50X There is a 1.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 902173024 3.6195417302490895 40.73123991712837 chr2 243199373 516949587 2.125620558240502 23.72556688358221 chr3 198022430 410237820 2.0716734967851873 23.475421681361368 chr4 191154276 289668699 1.5153660439173227 22.38758386557935 chr5 180915260 400102740 2.211547771039325 37.051450285496095 chr6 171115067 403801032 2.359821604721693 27.930476717028046 chr7 159138663 428058087 2.68984342918603 35.75976824802265 chr8 146364022 363788344 2.485503876082334 50.012779539276195 chr9 141213431 358400158 2.53800332915925 30.829087469241877 chr10 135534747 288143718 2.125976728314548 22.36738431164971 chr11 135006516 413238728 3.0608798763461165 33.85465510175127 chr12 133851895 380535238 2.8429574194672402 30.77663585129113 chr13 115169878 134778420 1.1702575564072404 15.515856578435601 chr14 107349540 191102337 1.7801877586061383 21.12530361378308 chr15 102531392 323191503 3.152122454360124 32.034944115985 chr16 90354753 286896028 3.1752178880949407 29.954985422934847 chr17 81195210 395388895 4.869608625927564 43.07190001572575 chr18 78077248 118697665 1.5202593334232273 17.650859681332513 chr19 59128983 478129828 8.086217684481399 58.7409077083476 chr20 63025520 181268393 2.876111026136714 30.01725195250751 chr21 48129895 98984554 2.0566127144054644 39.9904623292909 chr22 51304566 155459422 3.0301283905218104 28.713869372408052 chrMT 16571 562 0.033914670206988115 0.20625367936418154 chrX 155270560 459961130 2.9623202878897326 46.49352437945836 chrY 59373566 6508221 0.10961479052816198 7.384611047108113