BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504672.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 91,259,870 number of mapped reads = 90,772,576 (99.47%) number of supplementary alignments = 1,108,427 (1.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 45,474,241 number of mapped paired reads (second in pair) = 45,298,335 number of mapped paired reads (both in pair) = 90,551,326 number of mapped paired reads (singletons) = 221,250 number of mapped bases = 8,438,821,914 bp number of sequenced bases = 8,431,955,019 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,992,721 duplication rate = 25.73% >>>>>>> Insert size mean insert size = 30,838.5047 std insert size = 1,641,719.8169 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 53.0628 >>>>>>> ACTG content number of A's = 2,544,311,389 bp (30.17%) number of C's = 1,667,210,343 bp (19.77%) number of T's = 2,571,874,727 bp (30.5%) number of G's = 1,643,866,341 bp (19.5%) number of N's = 4,692,219 bp (0.06%) GC percentage = 39.27% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 83,763,640 number of insertions = 2,648,558 mapped reads with insertion percentage = 2.85% number of deletions = 2,814,240 mapped reads with deletion percentage = 3.02% homopolymer indels = 37.93% >>>>>>> Coverage mean coverageData = 2.726X std coverageData = 344.4743X There is a 32.36% of reference with a coverageData >= 1X There is a 23.59% of reference with a coverageData >= 2X There is a 16.75% of reference with a coverageData >= 3X There is a 13.25% of reference with a coverageData >= 4X There is a 10.74% of reference with a coverageData >= 5X There is a 8.99% of reference with a coverageData >= 6X There is a 7.66% of reference with a coverageData >= 7X There is a 6.63% of reference with a coverageData >= 8X There is a 5.81% of reference with a coverageData >= 9X There is a 5.15% of reference with a coverageData >= 10X There is a 4.6% of reference with a coverageData >= 11X There is a 4.14% of reference with a coverageData >= 12X There is a 3.75% of reference with a coverageData >= 13X There is a 3.42% of reference with a coverageData >= 14X There is a 3.13% of reference with a coverageData >= 15X There is a 2.88% of reference with a coverageData >= 16X There is a 2.66% of reference with a coverageData >= 17X There is a 2.46% of reference with a coverageData >= 18X There is a 2.29% of reference with a coverageData >= 19X There is a 2.13% of reference with a coverageData >= 20X There is a 1.99% of reference with a coverageData >= 21X There is a 1.87% of reference with a coverageData >= 22X There is a 1.75% of reference with a coverageData >= 23X There is a 1.65% of reference with a coverageData >= 24X There is a 1.55% of reference with a coverageData >= 25X There is a 1.47% of reference with a coverageData >= 26X There is a 1.39% of reference with a coverageData >= 27X There is a 1.32% of reference with a coverageData >= 28X There is a 1.25% of reference with a coverageData >= 29X There is a 1.19% of reference with a coverageData >= 30X There is a 1.13% of reference with a coverageData >= 31X There is a 1.08% of reference with a coverageData >= 32X There is a 1.03% of reference with a coverageData >= 33X There is a 0.99% of reference with a coverageData >= 34X There is a 0.94% of reference with a coverageData >= 35X There is a 0.9% of reference with a coverageData >= 36X There is a 0.87% of reference with a coverageData >= 37X There is a 0.83% of reference with a coverageData >= 38X There is a 0.8% of reference with a coverageData >= 39X There is a 0.77% of reference with a coverageData >= 40X There is a 0.74% of reference with a coverageData >= 41X There is a 0.71% of reference with a coverageData >= 42X There is a 0.68% of reference with a coverageData >= 43X There is a 0.66% of reference with a coverageData >= 44X There is a 0.64% of reference with a coverageData >= 45X There is a 0.62% of reference with a coverageData >= 46X There is a 0.59% of reference with a coverageData >= 47X There is a 0.57% of reference with a coverageData >= 48X There is a 0.56% of reference with a coverageData >= 49X There is a 0.54% of reference with a coverageData >= 50X There is a 0.52% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 581396552 2.332578148320842 34.050760853737174 chr2 243199373 591826319 2.4335026513411284 14.015044984857417 chr3 198022430 505099998 2.550721138004417 24.799994149272173 chr4 191154276 540762211 2.8289307585251193 46.52979235273864 chr5 180915260 492201760 2.720620471705925 16.44550139847661 chr6 171115067 468419413 2.7374527632917327 28.107309115173866 chr7 159138663 392980939 2.4694246614350406 13.814087333100904 chr8 146364022 363401196 2.482858772492601 8.975907902562028 chr9 141213431 370296988 2.6222504855079967 32.97604126711713 chr10 135534747 318302517 2.3484938294089264 36.22865653163618 chr11 135006516 298573859 2.2115514705971675 12.992818309573545 chr12 133851895 369543286 2.760837162596764 30.1423542561437 chr13 115169878 274210419 2.3809213290996105 42.87677510371232 chr14 107349540 222767117 2.075156698389206 14.110446591934934 chr15 102531392 218307185 2.129174106989594 15.748497491226908 chr16 90354753 165678362 1.833643018204034 9.117332694431525 chr17 81195210 242137061 2.9821594278775803 129.32092373864063 chr18 78077248 181471474 2.3242555116696737 11.77945117567857 chr19 59128983 74740287 1.2640211823024252 6.381232463501039 chr20 63025520 106299121 1.6866044262705011 6.687930139724511 chr21 48129895 87671719 1.8215647260398138 10.989194763404344 chr22 51304566 42881857 0.8358292515328948 3.2642986037401465 chrMT 16571 1949 0.11761511073562247 0.7466863365219814 chrX 155270560 1522397617 9.804805347517263 1531.3463841671594 chrY 59373566 7452708 0.12552232419390139 1.7077151886339212