BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432713.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 401,666,604 number of mapped reads = 401,497,524 (99.96%) number of supplementary alignments = 197,061 (0.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 200,753,190 number of mapped paired reads (second in pair) = 200,744,334 number of mapped paired reads (both in pair) = 401,439,844 number of mapped paired reads (singletons) = 57,680 number of mapped bases = 55,552,211,665 bp number of sequenced bases = 55,497,121,826 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 193,573,363 duplication rate = 31.68% >>>>>>> Insert size mean insert size = 53,058.3635 std insert size = 2,271,622.1117 median insert size = 279 >>>>>>> Mapping quality mean mapping quality = 55.3701 >>>>>>> ACTG content number of A's = 15,197,037,093 bp (27.38%) number of C's = 12,064,515,227 bp (21.74%) number of T's = 15,052,304,344 bp (27.12%) number of G's = 13,182,981,085 bp (23.75%) number of N's = 284,077 bp (0%) GC percentage = 45.49% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 497,325,820 number of insertions = 11,569,756 mapped reads with insertion percentage = 2.81% number of deletions = 38,172,094 mapped reads with deletion percentage = 9.06% homopolymer indels = 52.22% >>>>>>> Coverage mean coverageData = 17.945X std coverageData = 53.3759X There is a 58.86% of reference with a coverageData >= 1X There is a 51.45% of reference with a coverageData >= 2X There is a 46.28% of reference with a coverageData >= 3X There is a 42.35% of reference with a coverageData >= 4X There is a 39.18% of reference with a coverageData >= 5X There is a 36.53% of reference with a coverageData >= 6X There is a 34.27% of reference with a coverageData >= 7X There is a 32.3% of reference with a coverageData >= 8X There is a 30.57% of reference with a coverageData >= 9X There is a 29.04% of reference with a coverageData >= 10X There is a 27.65% of reference with a coverageData >= 11X There is a 26.4% of reference with a coverageData >= 12X There is a 25.26% of reference with a coverageData >= 13X There is a 24.22% of reference with a coverageData >= 14X There is a 23.26% of reference with a coverageData >= 15X There is a 22.37% of reference with a coverageData >= 16X There is a 21.55% of reference with a coverageData >= 17X There is a 20.78% of reference with a coverageData >= 18X There is a 20.06% of reference with a coverageData >= 19X There is a 19.39% of reference with a coverageData >= 20X There is a 18.76% of reference with a coverageData >= 21X There is a 18.17% of reference with a coverageData >= 22X There is a 17.61% of reference with a coverageData >= 23X There is a 17.09% of reference with a coverageData >= 24X There is a 16.59% of reference with a coverageData >= 25X There is a 16.11% of reference with a coverageData >= 26X There is a 15.67% of reference with a coverageData >= 27X There is a 15.24% of reference with a coverageData >= 28X There is a 14.83% of reference with a coverageData >= 29X There is a 14.45% of reference with a coverageData >= 30X There is a 14.07% of reference with a coverageData >= 31X There is a 13.72% of reference with a coverageData >= 32X There is a 13.38% of reference with a coverageData >= 33X There is a 13.06% of reference with a coverageData >= 34X There is a 12.74% of reference with a coverageData >= 35X There is a 12.44% of reference with a coverageData >= 36X There is a 12.16% of reference with a coverageData >= 37X There is a 11.88% of reference with a coverageData >= 38X There is a 11.61% of reference with a coverageData >= 39X There is a 11.36% of reference with a coverageData >= 40X There is a 11.11% of reference with a coverageData >= 41X There is a 10.87% of reference with a coverageData >= 42X There is a 10.64% of reference with a coverageData >= 43X There is a 10.42% of reference with a coverageData >= 44X There is a 10.21% of reference with a coverageData >= 45X There is a 10% of reference with a coverageData >= 46X There is a 9.8% of reference with a coverageData >= 47X There is a 9.6% of reference with a coverageData >= 48X There is a 9.42% of reference with a coverageData >= 49X There is a 9.24% of reference with a coverageData >= 50X There is a 9.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4586385056 18.400696606489095 53.549283513099574 chr2 243199373 3892217232 16.004223958258315 51.48554290582765 chr3 198022430 3607652332 18.21840249107134 48.85754260367484 chr4 191154276 2148190269 11.237992233037989 35.96934525236808 chr5 180915260 3175223046 17.550885679848122 49.21511105326456 chr6 171115067 2744596686 16.039479948308703 46.57661198196366 chr7 159138663 4101300119 25.771864873591404 68.06624543080683 chr8 146364022 4925833961 33.65467752040867 84.81658426408 chr9 141213431 2478019751 17.548045773351404 56.777939537978355 chr10 135534747 2673328220 19.724301547558134 52.84312977051166 chr11 135006516 2781419204 20.602110819599254 55.21865938049456 chr12 133851895 2692360144 20.11447162552312 54.67410761332968 chr13 115169878 1125323497 9.770988009555763 31.835521559733152 chr14 107349540 1710262831 15.931720163868425 47.29802679219809 chr15 102531392 1972326768 19.236320989380502 55.828369908854484 chr16 90354753 1958799076 21.678982133900583 64.13168471514878 chr17 81195210 1705961491 21.010617387404995 55.76018745802197 chr18 78077248 1079628299 13.82769406780321 42.456120504197656 chr19 59128983 1411234814 23.86705710801757 65.19575029928428 chr20 63025520 1562749767 24.79550770862343 62.378592310117654 chr21 48129895 663130202 13.777927460676986 53.74061431650109 chr22 51304566 811970573 15.826477764181847 49.43062367527731 chrMT 16571 9796889 591.206867418985 1019.0810097234755 chrX 155270560 1564238093 10.074273532600127 29.98371706527364 chrY 59373566 170263345 2.8676624375231228 23.172609628422226