BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549153.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 15,914,571 number of mapped reads = 13,945,588 (87.63%) number of secondary alignments = 0 number of mapped bases = 553,630,170 bp number of sequenced bases = 553,577,839 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 928,491 duplication rate = 5.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1784 >>>>>>> ACTG content number of A's = 158,974,047 bp (28.72%) number of C's = 116,019,262 bp (20.96%) number of T's = 161,588,996 bp (29.19%) number of G's = 116,883,122 bp (21.11%) number of N's = 112,412 bp (0.02%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,693,492 number of insertions = 13,791 mapped reads with insertion percentage = 0.1% number of deletions = 41,689 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.7% >>>>>>> Coverage mean coverageData = 0.1788X std coverageData = 0.9162X There is a 11.41% of reference with a coverageData >= 1X There is a 3.84% of reference with a coverageData >= 2X There is a 1.42% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% 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 45261275 0.18158941718343802 1.6017531374487557 chr2 243199373 48353601 0.19882288512314544 0.9005150171387334 chr3 198022430 36975559 0.1867240948411753 0.619282771121866 chr4 191154276 35845881 0.1875233018590701 0.6528334229658187 chr5 180915260 33739133 0.18649136065139005 0.629797440268226 chr6 171115067 32341231 0.18900282463145107 0.7019013744952711 chr7 159138663 31291825 0.19663244877204983 1.2952290884941426 chr8 146364022 28162373 0.1924132216044186 1.0218332741588423 chr9 141213431 23809422 0.1686059309755033 0.8540128130594963 chr10 135534747 26652259 0.1966452115781055 0.860209606548234 chr11 135006516 25752042 0.19074665996121254 0.8143507943852217 chr12 133851895 25578015 0.19109191543384574 0.6525220714172044 chr13 115169878 17649912 0.15325111310789094 0.5578458689217392 chr14 107349540 17493643 0.16295964565847232 0.7326277845676763 chr15 102531392 16856060 0.1643990164495182 0.5817168159143524 chr16 90354753 16752025 0.1854028088594299 0.68361881168402 chr17 81195210 15882860 0.19561326339324697 0.6944658545928487 chr18 78077248 14937283 0.19131415851132458 1.654608062042614 chr19 59128983 11443712 0.1935381164935646 1.4105564817167122 chr20 63025520 12410141 0.1969066022779344 0.6828463557231754 chr21 48129895 7155234 0.14866506565202356 0.6525112842159826 chr22 51304566 6806087 0.1326604536524098 0.5665296486000299 chrMT 16571 10050 0.6064812021000543 1.0539513555576905 chrX 155270560 18252424 0.11755238082480027 0.5899717459492687 chrY 59373566 4218123 0.07104378739858745 0.5147464881084239