BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231878.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,212,537 number of mapped reads = 1,062,044 (87.59%) number of supplementary alignments = 5,931 (0.49%) number of secondary alignments = 0 number of mapped bases = 70,793,523 bp number of sequenced bases = 70,757,045 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,892 duplication rate = 2.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3071 >>>>>>> ACTG content number of A's = 19,983,466 bp (28.24%) number of C's = 12,467,262 bp (17.62%) number of T's = 22,860,844 bp (32.31%) number of G's = 15,441,903 bp (21.82%) number of N's = 3,570 bp (0.01%) GC percentage = 39.44% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 524,271 number of insertions = 5,397 mapped reads with insertion percentage = 0.5% number of deletions = 21,226 mapped reads with deletion percentage = 1.98% homopolymer indels = 46.28% >>>>>>> Coverage mean coverageData = 0.0229X std coverageData = 0.2395X There is a 2.09% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 5280609 0.021185941197715212 0.3617687514379132 chr2 243199373 6191189 0.025457257243833437 0.26522458579320307 chr3 198022430 7597730 0.0383680272987257 0.20866834000703377 chr4 191154276 3025466 0.01582735193430881 0.13981166299588732 chr5 180915260 4138243 0.022873930037742532 0.16228746662554105 chr6 171115067 4816735 0.028149099225727444 0.2038678358165949 chr7 159138663 4671056 0.029352112880325004 0.31797587827207235 chr8 146364022 4002648 0.027347212418090013 0.47423454005871063 chr9 141213431 2982977 0.02112389012062174 0.19939892362084358 chr10 135534747 3738227 0.02758131831684461 0.22567607981165083 chr11 135006516 2508625 0.01858151053983202 0.18784932690256628 chr12 133851895 2289981 0.017108319609520656 0.1420355446539988 chr13 115169878 3433916 0.029816094795203307 0.18475298556695496 chr14 107349540 2705968 0.0252070758756861 0.18015735005234437 chr15 102531392 924640 0.009018116129741027 0.10344167197050544 chr16 90354753 2562023 0.028355154708906125 0.19229504841987258 chr17 81195210 1694071 0.020864174130469027 0.16064514490051485 chr18 78077248 1174101 0.015037684217558488 0.3540507040673078 chr19 59128983 1478497 0.025004607300619392 0.24809542297975765 chr20 63025520 1596212 0.025326439194789666 0.1748671109319339 chr21 48129895 1343888 0.027922105377541338 0.18227481500819184 chr22 51304566 551285 0.01074533989820711 0.10899416247940169 chrMT 16571 20207 1.2194194677448555 1.4781494716077523 chrX 155270560 1927861 0.012416139930196683 0.1315440609927361 chrY 59373566 137368 0.0023136221934185325 0.06119828151740172