BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927036.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 44,891,440 number of mapped reads = 44,165,811 (98.38%) number of supplementary alignments = 254,624 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 22,211,093 number of mapped paired reads (second in pair) = 21,954,718 number of mapped paired reads (both in pair) = 43,738,550 number of mapped paired reads (singletons) = 427,261 number of mapped bases = 4,191,352,248 bp number of sequenced bases = 4,188,215,189 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,746,397 duplication rate = 6.5% >>>>>>> Insert size mean insert size = 69,575.6585 std insert size = 2,587,299.2024 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.6891 >>>>>>> ACTG content number of A's = 1,224,726,006 bp (29.24%) number of C's = 818,925,359 bp (19.55%) number of T's = 1,238,376,628 bp (29.57%) number of G's = 905,509,034 bp (21.62%) number of N's = 678,162 bp (0.02%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 45,823,885 number of insertions = 678,976 mapped reads with insertion percentage = 1.51% number of deletions = 2,251,636 mapped reads with deletion percentage = 4.96% homopolymer indels = 53.21% >>>>>>> Coverage mean coverageData = 1.3539X std coverageData = 5.6014X There is a 40.16% of reference with a coverageData >= 1X There is a 26.19% of reference with a coverageData >= 2X There is a 17.64% of reference with a coverageData >= 3X There is a 12.4% of reference with a coverageData >= 4X There is a 8.91% of reference with a coverageData >= 5X There is a 6.53% of reference with a coverageData >= 6X There is a 4.86% of reference with a coverageData >= 7X There is a 3.65% of reference with a coverageData >= 8X There is a 2.78% of reference with a coverageData >= 9X There is a 2.13% of reference with a coverageData >= 10X There is a 1.64% of reference with a coverageData >= 11X There is a 1.28% of reference with a coverageData >= 12X There is a 1% of reference with a coverageData >= 13X There is a 0.79% of reference with a coverageData >= 14X There is a 0.62% of reference with a coverageData >= 15X There is a 0.5% of reference with a coverageData >= 16X There is a 0.4% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.17% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 341256059 1.3691282197447363 7.934001222958333 chr2 243199373 367977582 1.513069616343131 8.779062156101189 chr3 198022430 289817390 1.4635583958847491 2.765290809011658 chr4 191154276 260597491 1.363283607634286 4.200100146464105 chr5 180915260 261724036 1.4466664448316853 2.6992300210835727 chr6 171115067 238044598 1.3911375670968822 2.7124479527600354 chr7 159138663 215658904 1.3551634777778672 3.8059427406168234 chr8 146364022 216725332 1.4807281805907193 3.4248069345008285 chr9 141213431 181240347 1.283449780354108 7.591271768177929 chr10 135534747 206988549 1.5271991395682467 12.054038461868865 chr11 135006516 195674591 1.449371458485752 4.869782778604511 chr12 133851895 189749955 1.4176112710245903 2.72762509903148 chr13 115169878 126589971 1.0991586793206467 2.358075649853086 chr14 107349540 129187710 1.2034304944390073 2.642410498824398 chr15 102531392 121241247 1.1824792840030884 2.559723434393345 chr16 90354753 123324647 1.3648938534533983 6.706571095089938 chr17 81195210 103040457 1.269046006531666 4.408258495950858 chr18 78077248 112737525 1.4439228826302895 7.837687784908133 chr19 59128983 60724363 1.02698135362822 4.310331659641376 chr20 63025520 96752033 1.5351247082134347 3.149653362426587 chr21 48129895 52525144 1.0913205607450422 3.5886144485050604 chr22 51304566 47881982 0.9332889006409293 2.383530740118936 chrMT 16571 334192 20.16728018828073 16.06098036894349 chrX 155270560 244165815 1.5725184155966205 3.623711915804001 chrY 59373566 7392328 0.12450537331714251 5.576668835392609