BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21671992.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 418,210,598 number of mapped reads = 402,961,623 (96.35%) number of supplementary alignments = 5,781,313 (1.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 202,112,221 number of mapped paired reads (second in pair) = 200,849,402 number of mapped paired reads (both in pair) = 399,188,664 number of mapped paired reads (singletons) = 3,772,959 number of mapped bases = 54,225,446,713 bp number of sequenced bases = 54,195,229,810 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 213,449,130 duplication rate = 36.53% >>>>>>> Insert size mean insert size = 168,578.1276 std insert size = 4,074,009.0932 median insert size = 314 >>>>>>> Mapping quality mean mapping quality = 53.5948 >>>>>>> ACTG content number of A's = 14,346,043,000 bp (26.47%) number of C's = 10,900,279,560 bp (20.11%) number of T's = 15,764,343,640 bp (29.09%) number of G's = 13,184,492,261 bp (24.33%) number of N's = 71,349 bp (0%) GC percentage = 44.44% >>>>>>> Mismatches and indels general error rate = 0.0126 number of mismatches = 663,994,428 number of insertions = 8,664,966 mapped reads with insertion percentage = 2.05% number of deletions = 15,714,368 mapped reads with deletion percentage = 3.77% homopolymer indels = 46.28% >>>>>>> Coverage mean coverageData = 17.5164X std coverageData = 284.5282X There is a 59.12% of reference with a coverageData >= 1X There is a 52.69% of reference with a coverageData >= 2X There is a 48.21% of reference with a coverageData >= 3X There is a 44.82% of reference with a coverageData >= 4X There is a 42.02% of reference with a coverageData >= 5X There is a 39.64% of reference with a coverageData >= 6X There is a 37.55% of reference with a coverageData >= 7X There is a 35.7% of reference with a coverageData >= 8X There is a 34.03% of reference with a coverageData >= 9X There is a 32.52% of reference with a coverageData >= 10X There is a 31.13% of reference with a coverageData >= 11X There is a 29.85% of reference with a coverageData >= 12X There is a 28.67% of reference with a coverageData >= 13X There is a 27.56% of reference with a coverageData >= 14X There is a 26.53% of reference with a coverageData >= 15X There is a 25.57% of reference with a coverageData >= 16X There is a 24.66% of reference with a coverageData >= 17X There is a 23.8% of reference with a coverageData >= 18X There is a 22.99% of reference with a coverageData >= 19X There is a 22.23% of reference with a coverageData >= 20X There is a 21.51% of reference with a coverageData >= 21X There is a 20.82% of reference with a coverageData >= 22X There is a 20.16% of reference with a coverageData >= 23X There is a 19.54% of reference with a coverageData >= 24X There is a 18.94% of reference with a coverageData >= 25X There is a 18.37% of reference with a coverageData >= 26X There is a 17.83% of reference with a coverageData >= 27X There is a 17.31% of reference with a coverageData >= 28X There is a 16.81% of reference with a coverageData >= 29X There is a 16.33% of reference with a coverageData >= 30X There is a 15.88% of reference with a coverageData >= 31X There is a 15.44% of reference with a coverageData >= 32X There is a 15.01% of reference with a coverageData >= 33X There is a 14.61% of reference with a coverageData >= 34X There is a 14.21% of reference with a coverageData >= 35X There is a 13.84% of reference with a coverageData >= 36X There is a 13.47% of reference with a coverageData >= 37X There is a 13.12% of reference with a coverageData >= 38X There is a 12.78% of reference with a coverageData >= 39X There is a 12.46% of reference with a coverageData >= 40X There is a 12.14% of reference with a coverageData >= 41X There is a 11.84% of reference with a coverageData >= 42X There is a 11.55% of reference with a coverageData >= 43X There is a 11.26% of reference with a coverageData >= 44X There is a 10.99% of reference with a coverageData >= 45X There is a 10.72% of reference with a coverageData >= 46X There is a 10.46% of reference with a coverageData >= 47X There is a 10.22% of reference with a coverageData >= 48X There is a 9.97% of reference with a coverageData >= 49X There is a 9.74% of reference with a coverageData >= 50X There is a 9.51% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2469625516 9.90820205820069 128.12863426853718 chr2 243199373 4938767028 20.30748256904429 657.0166346357181 chr3 198022430 3542622737 17.890007394616863 40.19378480886835 chr4 191154276 3281027257 17.164289105413474 77.96009441649917 chr5 180915260 2912282309 16.097493981436394 41.49238346860161 chr6 171115067 2983989252 17.4384950683507 351.9949911793107 chr7 159138663 2835417139 17.817273851295333 450.6787182552999 chr8 146364022 2856683346 19.51766087706991 90.58370774425183 chr9 141213431 2451537729 17.36051388058123 495.77737664856136 chr10 135534747 2627497315 19.386152799621193 88.89947143917823 chr11 135006516 2787169210 20.6447014009309 233.4743974861701 chr12 133851895 2445271593 18.268486919815366 43.979447441398776 chr13 115169878 1689578748 14.670318119117917 36.82720038485129 chr14 107349540 1700119251 15.837229027716374 180.5927152481512 chr15 102531392 1678505248 16.370647225778423 38.71579789899413 chr16 90354753 2020372195 22.360441791036713 154.508023775963 chr17 81195210 1663647765 20.489481645530567 326.01715935465336 chr18 78077248 1706351961 21.854663230445826 509.66700816321804 chr19 59128983 1186476907 20.065910942523736 87.15652545411479 chr20 63025520 1402769478 22.257166271694388 50.15863015853398 chr21 48129895 767795297 15.952565385816861 107.39822142102051 chr22 51304566 644108262 12.554599175441812 31.947070781466174 chrMT 16571 522517 31.532013758976525 88.93858257893932 chrX 155270560 3508115786 22.593566906695 182.26850004921445 chrY 59373566 125192867 2.1085623693210542 74.04077247119587