BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038479.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 = 21,953,774 number of mapped reads = 20,862,607 (95.03%) number of supplementary alignments = 317,205 (1.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,570,040 number of mapped paired reads (second in pair) = 10,292,567 number of mapped paired reads (both in pair) = 20,490,786 number of mapped paired reads (singletons) = 371,821 number of mapped bases = 2,799,291,180 bp number of sequenced bases = 2,797,420,149 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,083,930 duplication rate = 17.1% >>>>>>> Insert size mean insert size = 74,366.6 std insert size = 2,657,563.2264 median insert size = 235 >>>>>>> Mapping quality mean mapping quality = 53.3916 >>>>>>> ACTG content number of A's = 785,012,620 bp (28.06%) number of C's = 569,401,222 bp (20.35%) number of T's = 798,465,515 bp (28.54%) number of G's = 644,317,728 bp (23.03%) number of N's = 223,064 bp (0.01%) GC percentage = 43.39% >>>>>>> Mismatches and indels general error rate = 0.0132 number of mismatches = 35,673,476 number of insertions = 479,783 mapped reads with insertion percentage = 2.19% number of deletions = 971,989 mapped reads with deletion percentage = 4.5% homopolymer indels = 47.28% >>>>>>> Coverage mean coverageData = 0.9043X std coverageData = 11.7031X There is a 26.82% of reference with a coverageData >= 1X There is a 17.51% of reference with a coverageData >= 2X There is a 11.3% of reference with a coverageData >= 3X There is a 7.91% of reference with a coverageData >= 4X There is a 5.52% of reference with a coverageData >= 5X There is a 3.99% of reference with a coverageData >= 6X There is a 2.9% of reference with a coverageData >= 7X There is a 2.15% of reference with a coverageData >= 8X There is a 1.61% of reference with a coverageData >= 9X There is a 1.23% of reference with a coverageData >= 10X There is a 0.94% of reference with a coverageData >= 11X There is a 0.73% of reference with a coverageData >= 12X There is a 0.57% of reference with a coverageData >= 13X There is a 0.45% of reference with a coverageData >= 14X There is a 0.36% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.16% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% 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 249743289 1.0019765968807757 16.91524143933079 chr2 243199373 250672260 1.0307274106335793 14.641112310854052 chr3 198022430 189876324 0.9588627106535356 2.333552658341492 chr4 191154276 118889000 0.6219531285818581 11.475496005558885 chr5 180915260 190483575 1.0528883798967539 2.404078978113549 chr6 171115067 161804422 0.9455883975430405 10.729882710938835 chr7 159138663 136301893 0.8564976632988301 13.476680275689437 chr8 146364022 180264832 1.231619830725887 5.341772701308714 chr9 141213431 121705828 0.8618573115754123 20.79148361831553 chr10 135534747 147428077 1.0877511506329813 22.67573826141398 chr11 135006516 130294244 0.9650959661828471 9.081515146516878 chr12 133851895 116829716 0.872828255438595 2.345586151507395 chr13 115169878 89829650 0.7799752119212977 1.9855405635616048 chr14 107349540 90990655 0.847611037737097 2.2691452755589347 chr15 102531392 79353910 0.7739474560142517 2.043719104020756 chr16 90354753 86951283 0.9623321420622997 8.446567522780931 chr17 81195210 76495189 0.9421145533092408 19.897110406596294 chr18 78077248 113985533 1.4599071550267755 15.92172142327373 chr19 59128983 41078706 0.6947304674595874 7.631295102028377 chr20 63025520 78727191 1.249131954801801 4.391001475210846 chr21 48129895 28052979 0.5828597589917867 5.649671194623178 chr22 51304566 17608403 0.3432131752171922 1.3343516250461382 chrMT 16571 4381114 264.3844064932714 171.84015897669846 chrX 155270560 91835475 0.5914545229952156 2.8402212832170433 chrY 59373566 5707632 0.09613086065943892 12.106644518544677