BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081233.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,117,111 number of mapped reads = 1,870,328 (88.34%) number of supplementary alignments = 23,969 (1.13%) number of secondary alignments = 0 number of mapped bases = 122,715,065 bp number of sequenced bases = 122,668,788 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,815 duplication rate = 3.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6042 >>>>>>> ACTG content number of A's = 35,224,387 bp (28.72%) number of C's = 23,431,259 bp (19.1%) number of T's = 37,807,265 bp (30.82%) number of G's = 26,197,490 bp (21.36%) number of N's = 8,387 bp (0.01%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,063,007 number of insertions = 9,055 mapped reads with insertion percentage = 0.48% number of deletions = 28,329 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.52% >>>>>>> Coverage mean coverageData = 0.0396X std coverageData = 0.2869X There is a 3.21% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% 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 14562250 0.05842412725623661 0.4435894992258524 chr2 243199373 7408432 0.030462381167405395 0.28650158150290866 chr3 198022430 8691421 0.04389109354935196 0.25280916097706535 chr4 191154276 6601799 0.03453649658352398 0.22556827506556798 chr5 180915260 8614591 0.04761671845702789 0.2605314591727052 chr6 171115067 8983661 0.0525007011802181 0.31042339858378915 chr7 159138663 7675011 0.048228449675991054 0.3188746984749388 chr8 146364022 8508082 0.05812959963617288 0.3861163187003731 chr9 141213431 3753380 0.026579483080472706 0.2261329857730704 chr10 135534747 3846287 0.02837860463929593 0.2776467989043294 chr11 135006516 5026130 0.03722879568272097 0.2946996955950152 chr12 133851895 2491745 0.018615687136891115 0.16479602237697555 chr13 115169878 3816520 0.03313817871718159 0.21857854603595447 chr14 107349540 4362231 0.04063576797813945 0.24507288289239296 chr15 102531392 2346261 0.022883342888780835 0.18590692155202185 chr16 90354753 4293119 0.04751403614594575 0.2663697140386077 chr17 81195210 2025257 0.024943060064750125 0.19966390169207124 chr18 78077248 3176720 0.040686884865614115 0.3396486131879142 chr19 59128983 2693642 0.04555535819041569 0.3645421835815971 chr20 63025520 2342785 0.03717200587952309 0.23347042113572522 chr21 48129895 1830435 0.03803114467629734 0.2390090296244972 chr22 51304566 987197 0.01924189359676096 0.16212462975936523 chrMT 16571 41122 2.4815641783839237 2.393450423216288 chrX 155270560 8339631 0.05371031701051378 0.287704565653161 chrY 59373566 297356 0.005008222009100818 0.09993425208985308