BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548976.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 6,826,199 number of mapped reads = 2,955,479 (43.3%) number of secondary alignments = 0 number of mapped bases = 116,334,753 bp number of sequenced bases = 116,318,412 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,636 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8555 >>>>>>> ACTG content number of A's = 35,612,859 bp (30.62%) number of C's = 22,481,740 bp (19.33%) number of T's = 35,725,242 bp (30.71%) number of G's = 22,492,538 bp (19.34%) number of N's = 6,033 bp (0.01%) GC percentage = 38.66% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 396,005 number of insertions = 6,388 mapped reads with insertion percentage = 0.22% number of deletions = 13,137 mapped reads with deletion percentage = 0.44% homopolymer indels = 43.74% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 0.3207X There is a 3.1% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 9327388 0.03742172421708831 0.4897494126376589 chr2 243199373 10122518 0.041622303031184214 0.2986892444273955 chr3 198022430 8206588 0.04144271939294958 0.23956598961341968 chr4 191154276 8122848 0.042493676678203106 0.24993378516763204 chr5 180915260 7469360 0.041286511707193746 0.24100360123014936 chr6 171115067 7040117 0.04114258974050485 0.2642943245110149 chr7 159138663 6693928 0.04206349276668235 0.4295742061673172 chr8 146364022 6125002 0.041847729491882917 0.6251893235544829 chr9 141213431 4930465 0.03491498623810082 0.26432237895239236 chr10 135534747 5424657 0.04002410540523604 0.2698130401323486 chr11 135006516 5438660 0.04028442597540996 0.2794270809887082 chr12 133851895 5353514 0.03999580282371049 0.24245374571267272 chr13 115169878 3979401 0.03455244608316768 0.2190112345538904 chr14 107349540 3594656 0.033485527744226945 0.2452043077954983 chr15 102531392 3324371 0.03242295783909771 0.21002339544948917 chr16 90354753 3019148 0.03341437942949166 0.21865273141240002 chr17 81195210 2883608 0.03551450879922596 0.2290521364312785 chr18 78077248 3166559 0.04055674452050359 0.4089858571852455 chr19 59128983 2046558 0.03461175714792862 0.4226666262431045 chr20 63025520 2331318 0.03699006370752673 0.23078019396990826 chr21 48129895 1527200 0.031730798498521555 0.22588851450435557 chr22 51304566 1201839 0.02342557580547509 0.2077903421753807 chrMT 16571 5806 0.3503711302878523 0.6691448466159958 chrX 155270560 3989358 0.025692945269212657 0.2108396398926215 chrY 59373566 1009886 0.017009017110409034 0.21285106211390648