BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089713.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 18,383,780 number of mapped reads = 15,794,878 (85.92%) number of supplementary alignments = 627 (0%) number of secondary alignments = 0 number of mapped bases = 747,831,311 bp number of sequenced bases = 747,697,644 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,385,080 duplication rate = 12.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1481 >>>>>>> ACTG content number of A's = 218,188,686 bp (29.18%) number of C's = 152,809,711 bp (20.44%) number of T's = 217,676,062 bp (29.11%) number of G's = 159,012,865 bp (21.27%) number of N's = 10,320 bp (0%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 4,042,137 number of insertions = 29,583 mapped reads with insertion percentage = 0.19% number of deletions = 86,930 mapped reads with deletion percentage = 0.55% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.2416X std coverageData = 1.5712X There is a 10.24% of reference with a coverageData >= 1X There is a 5.25% of reference with a coverageData >= 2X There is a 3.02% of reference with a coverageData >= 3X There is a 1.84% of reference with a coverageData >= 4X There is a 1.16% of reference with a coverageData >= 5X There is a 0.74% of reference with a coverageData >= 6X There is a 0.49% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.22% of reference with a coverageData >= 9X There is a 0.15% 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 0.01% 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 61411712 0.24638539215515134 2.8328441566794527 chr2 243199373 60508738 0.24880301809001787 1.4719893993213538 chr3 198022430 53338621 0.26935646128572405 1.0355512961151092 chr4 191154276 49443171 0.2586558461292281 1.1317533108826798 chr5 180915260 44826172 0.2477744110695803 1.0059206209637273 chr6 171115067 44721577 0.2613538233894973 1.1334260014277606 chr7 159138663 41542341 0.26104492910060456 2.157510586219726 chr8 146364022 39356068 0.26889168159098553 2.120105582621703 chr9 141213431 31383522 0.22224176395799064 1.359523847872204 chr10 135534747 33186677 0.24485733536655363 1.4578101009712603 chr11 135006516 31801791 0.23555745264917435 1.4973204108615648 chr12 133851895 33631246 0.25125715254162073 1.0606961063066203 chr13 115169878 22301008 0.19363576993630227 0.8750076960556941 chr14 107349540 23213139 0.2162388306461304 0.9909104951925961 chr15 102531392 20139304 0.19642085811143575 0.8913228193437835 chr16 90354753 20501190 0.22689664150816727 1.0416123096997472 chr17 81195210 19697295 0.2425918351587489 1.1801209545442166 chr18 78077248 20671622 0.2647585888273111 2.875164265564399 chr19 59128983 13513778 0.22854744516745704 1.9746206614671762 chr20 63025520 16542606 0.26247472452428794 1.1268477174502287 chr21 48129895 9334365 0.19394110458790736 1.1101936048618453 chr22 51304566 7912443 0.1542249280502636 0.7948374391037254 chrMT 16571 27486 1.658680827952447 2.494801194543103 chrX 155270560 46395214 0.2988023872651712 1.2569182380860915 chrY 59373566 2430225 0.04093109381370154 1.083071120773262