BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617602.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 48,023,314 number of mapped reads = 47,100,633 (98.08%) number of supplementary alignments = 647,907 (1.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 23,775,172 number of mapped paired reads (second in pair) = 23,325,461 number of mapped paired reads (both in pair) = 46,525,248 number of mapped paired reads (singletons) = 575,385 number of mapped bases = 6,343,611,534 bp number of sequenced bases = 6,339,333,961 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,008,219 duplication rate = 23.74% >>>>>>> Insert size mean insert size = 78,558.1069 std insert size = 2,662,559.0106 median insert size = 279 >>>>>>> Mapping quality mean mapping quality = 53.5129 >>>>>>> ACTG content number of A's = 1,834,459,430 bp (28.94%) number of C's = 1,209,199,805 bp (19.07%) number of T's = 1,878,447,614 bp (29.63%) number of G's = 1,416,968,200 bp (22.35%) number of N's = 258,912 bp (0%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 71,033,680 number of insertions = 1,070,659 mapped reads with insertion percentage = 2.15% number of deletions = 2,249,411 mapped reads with deletion percentage = 4.6% homopolymer indels = 47.84% >>>>>>> Coverage mean coverageData = 2.0492X std coverageData = 28.9644X There is a 43.17% of reference with a coverageData >= 1X There is a 31.42% of reference with a coverageData >= 2X There is a 23.28% of reference with a coverageData >= 3X There is a 17.91% of reference with a coverageData >= 4X There is a 13.91% of reference with a coverageData >= 5X There is a 11% of reference with a coverageData >= 6X There is a 8.78% of reference with a coverageData >= 7X There is a 7.08% of reference with a coverageData >= 8X There is a 5.76% of reference with a coverageData >= 9X There is a 4.72% of reference with a coverageData >= 10X There is a 3.89% of reference with a coverageData >= 11X There is a 3.23% of reference with a coverageData >= 12X There is a 2.7% of reference with a coverageData >= 13X There is a 2.26% of reference with a coverageData >= 14X There is a 1.91% of reference with a coverageData >= 15X There is a 1.62% of reference with a coverageData >= 16X There is a 1.38% of reference with a coverageData >= 17X There is a 1.17% of reference with a coverageData >= 18X There is a 1.01% of reference with a coverageData >= 19X There is a 0.87% of reference with a coverageData >= 20X There is a 0.75% of reference with a coverageData >= 21X There is a 0.65% of reference with a coverageData >= 22X There is a 0.56% of reference with a coverageData >= 23X There is a 0.49% of reference with a coverageData >= 24X There is a 0.43% of reference with a coverageData >= 25X There is a 0.38% of reference with a coverageData >= 26X There is a 0.33% of reference with a coverageData >= 27X There is a 0.29% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 612821436 2.458655603510011 26.86906352607325 chr2 243199373 374348832 1.5392672578970834 23.791562356041897 chr3 198022430 268895869 1.3579061169989683 3.5326077981748845 chr4 191154276 388680797 2.033335613167241 24.74589057765912 chr5 180915260 360845547 1.9945556112845317 4.311610411660114 chr6 171115067 413898411 2.418830896989334 21.692942280519198 chr7 159138663 308518230 1.9386755184690725 29.556475809239814 chr8 146364022 490782132 3.353161011112417 9.31789754817262 chr9 141213431 246297554 1.7441510503345818 37.40494122956897 chr10 135534747 346184775 2.554214197190334 99.00894722750904 chr11 135006516 274378452 2.0323348837473887 23.945687708336557 chr12 133851895 332006365 2.4804009311933912 7.260779817713602 chr13 115169878 190445031 1.6536010483574533 3.5292125781016437 chr14 107349540 334106718 3.1123255674872943 5.995422116861208 chr15 102531392 105994079 1.0337719690765537 3.550466395422056 chr16 90354753 132208630 1.4632172144834483 20.704247581319212 chr17 81195210 172842409 2.1287266699599643 34.13645241617661 chr18 78077248 313887296 4.020214646909686 36.943735436900724 chr19 59128983 68815104 1.1638134212455506 13.400379974558257 chr20 63025520 82123332 1.3030171270304474 7.568804455648619 chr21 48129895 96379973 2.0024970551047327 11.762693268685158 chr22 51304566 56673149 1.104641427041796 3.1259880758525123 chrMT 16571 1438219 86.79132218936697 49.431059749915406 chrX 155270560 351674329 2.264913123260456 8.910001199792942 chrY 59373566 19364865 0.32615297184609054 23.167820214880518