BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617402.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,136,727 (94.18%) number of supplementary alignments = 495,109 (1.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,213,153 number of mapped paired reads (second in pair) = 14,923,574 number of mapped paired reads (both in pair) = 29,596,864 number of mapped paired reads (singletons) = 539,863 number of mapped bases = 2,971,003,056 bp number of sequenced bases = 2,970,331,980 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,432,212 duplication rate = 4.25% >>>>>>> Insert size mean insert size = 60,205.2238 std insert size = 2,349,030.4993 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 53.9099 >>>>>>> ACTG content number of A's = 883,644,492 bp (29.75%) number of C's = 599,057,897 bp (20.17%) number of T's = 877,450,342 bp (29.54%) number of G's = 609,560,251 bp (20.52%) number of N's = 618,998 bp (0.02%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 24,598,461 number of insertions = 249,029 mapped reads with insertion percentage = 0.81% number of deletions = 297,580 mapped reads with deletion percentage = 0.97% homopolymer indels = 44.95% >>>>>>> Coverage mean coverageData = 0.9597X std coverageData = 2.9573X There is a 29.68% of reference with a coverageData >= 1X There is a 17.03% of reference with a coverageData >= 2X There is a 10.92% of reference with a coverageData >= 3X There is a 7.56% of reference with a coverageData >= 4X There is a 5.5% of reference with a coverageData >= 5X There is a 4.14% of reference with a coverageData >= 6X There is a 3.21% of reference with a coverageData >= 7X There is a 2.54% of reference with a coverageData >= 8X There is a 2.05% of reference with a coverageData >= 9X There is a 1.68% of reference with a coverageData >= 10X There is a 1.39% of reference with a coverageData >= 11X There is a 1.16% of reference with a coverageData >= 12X There is a 0.99% of reference with a coverageData >= 13X There is a 0.84% of reference with a coverageData >= 14X There is a 0.73% of reference with a coverageData >= 15X There is a 0.63% of reference with a coverageData >= 16X There is a 0.55% of reference with a coverageData >= 17X There is a 0.48% of reference with a coverageData >= 18X There is a 0.42% of reference with a coverageData >= 19X There is a 0.37% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 191208588 0.7671338479834721 2.750521921923714 chr2 243199373 296079312 1.21743452027732 3.167863677063703 chr3 198022430 250288091 1.2639380851957023 3.4464244627838774 chr4 191154276 141292165 0.7391525209721178 2.2762638500056 chr5 180915260 189566209 1.0478176854732983 2.877722775494272 chr6 171115067 135793904 0.7935823909650224 2.6231571169001615 chr7 159138663 222265250 1.396676620313192 3.25167010289496 chr8 146364022 131195267 0.8963628165397095 3.277470672093483 chr9 141213431 118580032 0.8397220516510218 2.6296604155453647 chr10 135534747 95389263 0.7037993216602972 2.4489611878685573 chr11 135006516 220966586 1.6367105273644718 3.8697902898695964 chr12 133851895 141740015 1.0589317020875946 2.8268417337012797 chr13 115169878 128292329 1.1139399574600575 2.781996113070332 chr14 107349540 86282263 0.8037506541714106 2.925170088413555 chr15 102531392 68407818 0.6671890107568227 2.3916086391719333 chr16 90354753 75916030 0.8401996295645897 3.3843990952065037 chr17 81195210 92964071 1.1449452621650957 3.757160591931394 chr18 78077248 42388554 0.5429053288353606 2.019951999327989 chr19 59128983 43009656 0.7273870413093355 2.377639666354914 chr20 63025520 102233880 1.6221029195792434 4.83085677889446 chr21 48129895 40512602 0.8417346848564702 2.528820826653443 chr22 51304566 24423774 0.47605458742210194 2.1294844888766518 chrMT 16571 192565 11.620602256954921 5.594225617289704 chrX 155270560 129591826 0.8346194281774987 2.579710783102938 chrY 59373566 2423006 0.04080950771931064 0.6313555561118667