BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504627.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 = 304,888,020 number of mapped reads = 283,941,383 (93.13%) number of supplementary alignments = 2,814,021 (0.92%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 143,840,963 number of mapped paired reads (second in pair) = 140,100,420 number of mapped paired reads (both in pair) = 276,327,398 number of mapped paired reads (singletons) = 7,613,985 number of mapped bases = 27,113,827,028 bp number of sequenced bases = 27,088,107,222 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,770,343 duplication rate = 16.06% >>>>>>> Insert size mean insert size = 113,612.9641 std insert size = 3,143,701.7257 median insert size = 366 >>>>>>> Mapping quality mean mapping quality = 52.0458 >>>>>>> ACTG content number of A's = 7,257,438,215 bp (26.79%) number of C's = 6,228,049,267 bp (22.99%) number of T's = 7,315,484,483 bp (27.01%) number of G's = 6,282,595,957 bp (23.19%) number of N's = 4,539,300 bp (0.02%) GC percentage = 46.19% >>>>>>> Mismatches and indels general error rate = 0.0136 number of mismatches = 336,956,689 number of insertions = 8,003,994 mapped reads with insertion percentage = 2.61% number of deletions = 7,730,623 mapped reads with deletion percentage = 2.53% homopolymer indels = 33.59% >>>>>>> Coverage mean coverageData = 8.7586X std coverageData = 206.6161X There is a 82.29% of reference with a coverageData >= 1X There is a 73.1% of reference with a coverageData >= 2X There is a 64.47% of reference with a coverageData >= 3X There is a 56.91% of reference with a coverageData >= 4X There is a 50.29% of reference with a coverageData >= 5X There is a 44.54% of reference with a coverageData >= 6X There is a 39.51% of reference with a coverageData >= 7X There is a 35.1% of reference with a coverageData >= 8X There is a 31.22% of reference with a coverageData >= 9X There is a 27.79% of reference with a coverageData >= 10X There is a 24.76% of reference with a coverageData >= 11X There is a 22.08% of reference with a coverageData >= 12X There is a 19.7% of reference with a coverageData >= 13X There is a 17.6% of reference with a coverageData >= 14X There is a 15.72% of reference with a coverageData >= 15X There is a 14.06% of reference with a coverageData >= 16X There is a 12.58% of reference with a coverageData >= 17X There is a 11.27% of reference with a coverageData >= 18X There is a 10.1% of reference with a coverageData >= 19X There is a 9.06% of reference with a coverageData >= 20X There is a 8.14% of reference with a coverageData >= 21X There is a 7.32% of reference with a coverageData >= 22X There is a 6.59% of reference with a coverageData >= 23X There is a 5.94% of reference with a coverageData >= 24X There is a 5.36% of reference with a coverageData >= 25X There is a 4.84% of reference with a coverageData >= 26X There is a 4.38% of reference with a coverageData >= 27X There is a 3.97% of reference with a coverageData >= 28X There is a 3.6% of reference with a coverageData >= 29X There is a 3.28% of reference with a coverageData >= 30X There is a 2.98% of reference with a coverageData >= 31X There is a 2.72% of reference with a coverageData >= 32X There is a 2.49% of reference with a coverageData >= 33X There is a 2.28% of reference with a coverageData >= 34X There is a 2.09% of reference with a coverageData >= 35X There is a 1.92% of reference with a coverageData >= 36X There is a 1.77% of reference with a coverageData >= 37X There is a 1.64% of reference with a coverageData >= 38X There is a 1.52% of reference with a coverageData >= 39X There is a 1.41% of reference with a coverageData >= 40X There is a 1.31% of reference with a coverageData >= 41X There is a 1.22% of reference with a coverageData >= 42X There is a 1.14% of reference with a coverageData >= 43X There is a 1.07% of reference with a coverageData >= 44X There is a 1% of reference with a coverageData >= 45X There is a 0.94% of reference with a coverageData >= 46X There is a 0.89% of reference with a coverageData >= 47X There is a 0.84% of reference with a coverageData >= 48X There is a 0.8% of reference with a coverageData >= 49X There is a 0.76% of reference with a coverageData >= 50X There is a 0.72% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1908110515 7.655389211648143 60.3212756210761 chr2 243199373 2066541914 8.497315961419028 238.4375400411231 chr3 198022430 1373007078 6.9335937247108825 23.37298017304798 chr4 191154276 1957472727 10.240276953051263 531.9001706423359 chr5 180915260 1656057648 9.153775353168108 33.865148666007975 chr6 171115067 793512438 4.637303142919612 25.9549157480233 chr7 159138663 1269642769 7.978216890008683 34.412668530775946 chr8 146364022 1491661312 10.191447950234656 139.003003381012 chr9 141213431 707175136 5.007846144606457 75.00111778879345 chr10 135534747 2026797932 14.954083560579488 475.9649047883231 chr11 135006516 1098469892 8.136421296880219 25.360275513550164 chr12 133851895 1019705919 7.6181657271269865 19.94819319754414 chr13 115169878 411405729 3.5721643206047333 11.417819915921461 chr14 107349540 694353232 6.468152839779285 30.009599740229955 chr15 102531392 927679100 9.047756807983257 16.863944233354225 chr16 90354753 1453579286 16.087468979080715 202.59241981476507 chr17 81195210 885272297 10.903011359906575 72.47544299097156 chr18 78077248 458628693 5.874037632576394 278.15500244815445 chr19 59128983 1069406287 18.08599155172346 40.92448085543853 chr20 63025520 800899358 12.707540659720063 130.0937095266776 chr21 48129895 519199941 10.78747296249036 169.76375510218833 chr22 51304566 484011192 9.434076335427923 30.301464630803704 chrMT 16571 9415047 568.1640818297025 255.87891720617995 chrX 155270560 1545450905 9.953277073258446 21.372703002801387 chrY 59373566 486370681 8.19170404890284 506.5230540042656