BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038467.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 19,509,524 number of mapped reads = 18,917,042 (96.96%) number of supplementary alignments = 279,986 (1.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,564,821 number of mapped paired reads (second in pair) = 9,352,221 number of mapped paired reads (both in pair) = 18,654,738 number of mapped paired reads (singletons) = 262,304 number of mapped bases = 2,561,922,166 bp number of sequenced bases = 2,560,217,039 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,856,712 duplication rate = 14.5% >>>>>>> Insert size mean insert size = 77,914.8503 std insert size = 2,704,201.4138 median insert size = 247 >>>>>>> Mapping quality mean mapping quality = 53.4594 >>>>>>> ACTG content number of A's = 733,183,414 bp (28.64%) number of C's = 507,490,652 bp (19.82%) number of T's = 746,976,430 bp (29.18%) number of G's = 572,364,104 bp (22.36%) number of N's = 202,439 bp (0.01%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0127 number of mismatches = 31,529,779 number of insertions = 428,170 mapped reads with insertion percentage = 2.15% number of deletions = 868,190 mapped reads with deletion percentage = 4.43% homopolymer indels = 47.47% >>>>>>> Coverage mean coverageData = 0.8276X std coverageData = 11.4756X There is a 29.4% of reference with a coverageData >= 1X There is a 17.73% of reference with a coverageData >= 2X There is a 10.52% of reference with a coverageData >= 3X There is a 6.75% of reference with a coverageData >= 4X There is a 4.31% of reference with a coverageData >= 5X There is a 2.85% of reference with a coverageData >= 6X There is a 1.9% of reference with a coverageData >= 7X There is a 1.29% of reference with a coverageData >= 8X There is a 0.89% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.45% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.18% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 221049405 0.8868559850047475 15.619751804740975 chr2 243199373 231998936 0.9539454528116732 12.632269400802775 chr3 198022430 177682924 0.897286857857466 2.0262879877222346 chr4 191154276 109971045 0.575299947776214 9.215459850752639 chr5 180915260 178305374 0.9855739864066746 1.9829659957471417 chr6 171115067 153474105 0.8969058522473652 9.385768159603966 chr7 159138663 125318457 0.7874796396900733 11.842345020712749 chr8 146364022 164417797 1.1233484482955791 4.487732169243692 chr9 141213431 110199392 0.7803747222882786 18.206074431783797 chr10 135534747 140404560 1.0359303655172647 31.894840365471914 chr11 135006516 117386837 0.869490158534274 8.947669359645722 chr12 133851895 112158431 0.837929347208719 1.957263037812036 chr13 115169878 87860343 0.7628760620897767 1.6878972190082036 chr14 107349540 84056129 0.7830134064850208 1.8204602297292585 chr15 102531392 69146435 0.6743928240045741 1.615552950810799 chr16 90354753 78634754 0.8702890704598573 11.76098609325254 chr17 81195210 62271443 0.7669349337233071 14.066100732989456 chr18 78077248 103959897 1.331500528809622 12.835937541900245 chr19 59128983 32034869 0.5417794687928253 6.6054517396822465 chr20 63025520 67527733 1.0714347616647986 3.4778427066157978 chr21 48129895 24855269 0.5164205947260013 4.329881079848407 chr22 51304566 13805094 0.26908119639877665 1.0067165090802668 chrMT 16571 3902624 235.50926317059924 117.83285801261722 chrX 155270560 86564106 0.5575049513571665 2.560992981607796 chrY 59373566 4936207 0.08313812581174593 9.149242162614206