BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1954926.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 15,300,504 number of mapped reads = 14,975,434 (97.88%) number of supplementary alignments = 40,479 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,598,111 number of mapped paired reads (second in pair) = 7,377,323 number of mapped paired reads (both in pair) = 14,727,416 number of mapped paired reads (singletons) = 248,018 number of mapped bases = 1,348,558,694 bp number of sequenced bases = 1,347,704,733 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 869,482 duplication rate = 4.79% >>>>>>> Insert size mean insert size = 43,962.5859 std insert size = 2,116,834.4796 median insert size = 319 >>>>>>> Mapping quality mean mapping quality = 54.1321 >>>>>>> ACTG content number of A's = 381,827,848 bp (28.33%) number of C's = 259,158,742 bp (19.23%) number of T's = 382,843,711 bp (28.41%) number of G's = 323,839,769 bp (24.03%) number of N's = 34,663 bp (0%) GC percentage = 43.26% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 10,387,956 number of insertions = 210,776 mapped reads with insertion percentage = 1.39% number of deletions = 614,738 mapped reads with deletion percentage = 4.02% homopolymer indels = 53.85% >>>>>>> Coverage mean coverageData = 0.4356X std coverageData = 1.2924X There is a 23.2% of reference with a coverageData >= 1X There is a 9.31% of reference with a coverageData >= 2X There is a 4.48% of reference with a coverageData >= 3X There is a 2.4% of reference with a coverageData >= 4X There is a 1.39% of reference with a coverageData >= 5X There is a 0.85% of reference with a coverageData >= 6X There is a 0.54% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 115951477 0.4652003535028304 1.3548294124390194 chr2 243199373 135403712 0.5567601196077097 2.1584911307837666 chr3 198022430 89676875 0.45286220858919873 1.1223135953523207 chr4 191154276 79314431 0.41492365569682577 1.1484464731146202 chr5 180915260 81870821 0.452536845150597 1.1151528144404226 chr6 171115067 78102022 0.4564298361873651 1.13956682150565 chr7 159138663 66472465 0.4177015424592326 1.0794953277852226 chr8 146364022 70119026 0.47907282843047316 1.2218866587081563 chr9 141213431 56251677 0.3983450908433774 1.3653762278211676 chr10 135534747 65779604 0.4853338753050537 1.2543777752846588 chr11 135006516 65540553 0.48546214613819083 1.318890137539108 chr12 133851895 64992970 0.48555883351520723 1.196467112843079 chr13 115169878 39227835 0.34060846187576926 0.9614225612752115 chr14 107349540 45217631 0.4212186749938565 1.1431567544461456 chr15 102531392 43097941 0.42033898262104935 1.125187196854745 chr16 90354753 42223296 0.4673057542418383 1.473239126640506 chr17 81195210 38402038 0.4729594024080977 1.222979511953604 chr18 78077248 36589739 0.46863510097077193 1.4011616229826493 chr19 59128983 23245552 0.39313295816368093 1.1552955830886502 chr20 63025520 28219074 0.4477404391110141 1.1431274953193404 chr21 48129895 17411341 0.3617573028156409 1.4248566535238472 chr22 51304566 19393093 0.37799935779595134 1.0964442640610195 chrMT 16571 272351 16.435399191358396 12.655276323432682 chrX 155270560 38744452 0.24952864213280354 0.7723512929551314 chrY 59373566 7038718 0.1185496926359451 0.8027733922083056