BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082769.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 = 4,635,838 number of mapped reads = 4,095,995 (88.36%) number of supplementary alignments = 39,192 (0.85%) number of secondary alignments = 0 number of mapped bases = 279,889,671 bp number of sequenced bases = 279,782,923 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 226,887 duplication rate = 4.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4163 >>>>>>> ACTG content number of A's = 80,788,019 bp (28.88%) number of C's = 51,004,305 bp (18.23%) number of T's = 90,584,311 bp (32.38%) number of G's = 57,390,607 bp (20.51%) number of N's = 15,681 bp (0.01%) GC percentage = 38.74% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 2,462,783 number of insertions = 23,160 mapped reads with insertion percentage = 0.56% number of deletions = 62,539 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.16% >>>>>>> Coverage mean coverageData = 0.0904X std coverageData = 0.6309X There is a 6.56% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 25902732 0.10392243716817058 1.139750417568739 chr2 243199373 28429500 0.11689791650901994 0.7450982372391228 chr3 198022430 20555215 0.10380245813567686 0.41479521275318726 chr4 191154276 17111246 0.08951537134330179 0.4011078837963682 chr5 180915260 16041025 0.08866595885830747 0.38838535105811456 chr6 171115067 20246016 0.11831813735023111 0.6492128762978404 chr7 159138663 13647235 0.08575687857827485 0.4950890317161469 chr8 146364022 22103245 0.15101556173415348 1.1140656950595742 chr9 141213431 7858234 0.055647922045035506 0.5294729357033947 chr10 135534747 10192140 0.07519946158161199 0.488181488338764 chr11 135006516 11690161 0.08658960579354555 0.4924974916192429 chr12 133851895 8966639 0.06698925704413823 0.3461799216454154 chr13 115169878 6860121 0.059565236319864816 0.31387267998357116 chr14 107349540 6132508 0.05712654194885232 0.36430205236207935 chr15 102531392 5438221 0.05303957055415769 0.29529225095542827 chr16 90354753 9970775 0.11035141670964449 0.4667300958283375 chr17 81195210 6536097 0.08049855404031839 0.44958604724725015 chr18 78077248 11732287 0.150265119487818 1.1641409479880207 chr19 59128983 4634478 0.07837912585102301 0.7927636135292191 chr20 63025520 5332502 0.08460861568456714 0.3957409153777708 chr21 48129895 5548247 0.11527652408134278 0.45176807074399866 chr22 51304566 3361271 0.06551602054288891 0.32552373201572554 chrMT 16571 155246 9.36853539315672 6.337352472149613 chrX 155270560 11013905 0.07093363352331569 0.38805849084711264 chrY 59373566 430625 0.0072528067456820765 0.13831825268882253