BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617702.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 39,409,852 number of mapped reads = 38,006,063 (96.44%) number of supplementary alignments = 1,366,318 (3.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 19,334,190 number of mapped paired reads (second in pair) = 18,671,873 number of mapped paired reads (both in pair) = 37,121,564 number of mapped paired reads (singletons) = 884,499 number of mapped bases = 5,137,919,943 bp number of sequenced bases = 5,133,920,587 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,765,816 duplication rate = 16.63% >>>>>>> Insert size mean insert size = 257,528.9157 std insert size = 4,703,382.0354 median insert size = 277 >>>>>>> Mapping quality mean mapping quality = 52.7506 >>>>>>> ACTG content number of A's = 1,489,926,801 bp (29.02%) number of C's = 1,002,799,657 bp (19.53%) number of T's = 1,518,207,703 bp (29.57%) number of G's = 1,122,965,741 bp (21.87%) number of N's = 20,685 bp (0%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.0145 number of mismatches = 71,799,209 number of insertions = 974,380 mapped reads with insertion percentage = 2.39% number of deletions = 1,960,375 mapped reads with deletion percentage = 4.94% homopolymer indels = 45.07% >>>>>>> Coverage mean coverageData = 1.6597X std coverageData = 26.2251X There is a 33.33% of reference with a coverageData >= 1X There is a 24.04% of reference with a coverageData >= 2X There is a 17.97% of reference with a coverageData >= 3X There is a 13.92% of reference with a coverageData >= 4X There is a 10.94% of reference with a coverageData >= 5X There is a 8.72% of reference with a coverageData >= 6X There is a 7.03% of reference with a coverageData >= 7X There is a 5.72% of reference with a coverageData >= 8X There is a 4.69% of reference with a coverageData >= 9X There is a 3.88% of reference with a coverageData >= 10X There is a 3.22% of reference with a coverageData >= 11X There is a 2.69% of reference with a coverageData >= 12X There is a 2.27% of reference with a coverageData >= 13X There is a 1.91% of reference with a coverageData >= 14X There is a 1.63% of reference with a coverageData >= 15X There is a 1.39% of reference with a coverageData >= 16X There is a 1.19% of reference with a coverageData >= 17X There is a 1.02% of reference with a coverageData >= 18X There is a 0.88% of reference with a coverageData >= 19X There is a 0.76% of reference with a coverageData >= 20X There is a 0.66% of reference with a coverageData >= 21X There is a 0.58% of reference with a coverageData >= 22X There is a 0.51% of reference with a coverageData >= 23X There is a 0.45% of reference with a coverageData >= 24X There is a 0.39% of reference with a coverageData >= 25X There is a 0.35% of reference with a coverageData >= 26X There is a 0.31% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 376002180 1.5085305645035885 27.506287680107402 chr2 243199373 342248329 1.4072747177682896 24.155875075113116 chr3 198022430 491408092 2.4815779303384975 5.80381492915816 chr4 191154276 258409353 1.3518366337774208 20.29081184872478 chr5 180915260 258642132 1.429631375484854 3.9363716555076893 chr6 171115067 325449475 1.901933480819664 26.40090762984453 chr7 159138663 273221369 1.716876111998 21.99927350374682 chr8 146364022 457221213 3.12386341091392 13.217275021588538 chr9 141213431 231471887 1.6391633951589208 36.991067446352524 chr10 135534747 240457457 1.774138826554935 83.31139198500091 chr11 135006516 250047071 1.852111130695351 11.089934029263565 chr12 133851895 157756584 1.1785905907421035 6.925233651059815 chr13 115169878 113314719 0.9838919773797103 2.728899559793586 chr14 107349540 201027228 1.8726417272025573 4.700129671401599 chr15 102531392 99102942 0.9665619481690056 4.504939914582926 chr16 90354753 170712629 1.8893596997603435 27.627565615497097 chr17 81195210 121030512 1.4906114781894153 24.088818178654446 chr18 78077248 176167674 2.2563253510164705 30.487515416302664 chr19 59128983 63010977 1.0656529810431543 15.02383212532779 chr20 63025520 105053700 1.6668438435732065 7.248250644316871 chr21 48129895 50435859 1.047911261805163 10.085755126851332 chr22 51304566 33549147 0.6539212708670024 3.2049204816533736 chrMT 16571 783997 47.311387363466295 29.046471634462236 chrX 155270560 224058013 1.4430167122473185 6.1506427370202985 chrY 59373566 117337404 1.9762566391919258 42.81563645776902