BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093981.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 332,610 number of mapped reads = 303,532 (91.26%) number of supplementary alignments = 17,317 (5.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 152,652 number of mapped paired reads (second in pair) = 150,880 number of mapped paired reads (both in pair) = 300,550 number of mapped paired reads (singletons) = 2,982 number of mapped bases = 38,908,051 bp number of sequenced bases = 38,185,002 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 283,213 duplication rate = 49.09% >>>>>>> Insert size mean insert size = 906,309.8714 std insert size = 8,742,962.1568 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 41.951 >>>>>>> ACTG content number of A's = 10,030,437 bp (26.27%) number of C's = 8,936,167 bp (23.4%) number of T's = 9,518,324 bp (24.93%) number of G's = 9,699,658 bp (25.4%) number of N's = 416 bp (0%) GC percentage = 48.8% >>>>>>> Mismatches and indels general error rate = 0.0359 number of mismatches = 1,327,742 number of insertions = 21,861 mapped reads with insertion percentage = 7.07% number of deletions = 104,690 mapped reads with deletion percentage = 33.15% homopolymer indels = 29.54% >>>>>>> Coverage mean coverageData = 0.0126X std coverageData = 2.4443X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% 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 781760 0.003136441533680271 0.978024661998677 chr2 243199373 1863289 0.007661569916958626 2.4680539221513054 chr3 198022430 678434 0.0034260462312274424 1.1604538940843008 chr4 191154276 940450 0.00491984809170578 1.6204004814546704 chr5 180915260 263195 0.0014547971243553473 0.8812055863076681 chr6 171115067 653226 0.003817466290095892 1.1633709452542262 chr7 159138663 844499 0.005306686534120247 1.5641972051773536 chr8 146364022 484419 0.003309686310751969 1.0670440831928971 chr9 141213431 578140 0.004094086489549283 1.2708547531479162 chr10 135534747 749667 0.005531179395642359 1.6060778446262753 chr11 135006516 683447 0.0050623260287673815 1.3140644962368155 chr12 133851895 909014 0.0067911926088158854 1.6745289381654025 chr13 115169878 777547 0.006751305232779703 1.90755450997402 chr14 107349540 137911 0.0012846911127891187 0.4422358097420002 chr15 102531392 662497 0.006461406473443763 1.8024737268772502 chr16 90354753 206874 0.0022895751815070536 0.6539882357756664 chr17 81195210 888221 0.010939327578560362 2.522854498769849 chr18 78077248 224166 0.002871079677398466 0.7772361934313272 chr19 59128983 139973 0.0023672485623505483 0.6692206003220966 chr20 63025520 272765 0.004327850051852012 1.3599966636805956 chr21 48129895 85213 0.001770479657186038 0.30470363906985537 chr22 51304566 81313 0.0015849076668926505 0.3768553181205115 chrMT 16571 913961 55.1542453684147 225.2635505064293 chrX 155270560 24578733 0.15829615736556885 8.562969308272987 chrY 59373566 509337 0.008578514553092532 1.1761694764896542