BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084761.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 = 2,233,345 number of mapped reads = 1,911,449 (85.59%) number of supplementary alignments = 26,631 (1.19%) number of secondary alignments = 0 number of mapped bases = 125,219,945 bp number of sequenced bases = 125,178,542 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,412 duplication rate = 1.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3959 >>>>>>> ACTG content number of A's = 35,679,778 bp (28.5%) number of C's = 24,264,732 bp (19.38%) number of T's = 36,783,422 bp (29.38%) number of G's = 28,406,290 bp (22.69%) number of N's = 44,320 bp (0.04%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,075,135 number of insertions = 10,468 mapped reads with insertion percentage = 0.54% number of deletions = 24,927 mapped reads with deletion percentage = 1.29% homopolymer indels = 43.44% >>>>>>> Coverage mean coverageData = 0.0404X std coverageData = 0.4255X There is a 3.68% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 10032030 0.04024876632102754 0.7676746226638852 chr2 243199373 10656112 0.043816362964060766 0.5292070967904247 chr3 198022430 8368875 0.042262257866444726 0.21880684875566758 chr4 191154276 8038233 0.04205102375005203 0.23196936968264786 chr5 180915260 7659483 0.042337407026914145 0.22335400342684483 chr6 171115067 7246515 0.042348783932627046 0.2881694482272627 chr7 159138663 7049968 0.044300786918135666 0.6046773825381215 chr8 146364022 6377652 0.04357390506800913 0.4705706439581219 chr9 141213431 5293882 0.0374885162304427 0.4198300646849612 chr10 135534747 5837979 0.04307367025224904 0.3912372558913165 chr11 135006516 5698055 0.042205777682612 0.3789807390015874 chr12 133851895 5620021 0.04198686167274658 0.22557299087108143 chr13 115169878 3898387 0.033849015625422474 0.19506488350834517 chr14 107349540 3787908 0.03528574039534776 0.2523481819743884 chr15 102531392 3529058 0.03441929277620653 0.21564204951576407 chr16 90354753 3503319 0.03877293538725074 0.2611933662332789 chr17 81195210 3321404 0.04090640322255463 0.26503679563380617 chr18 78077248 3433230 0.04397222094713174 0.9503016546808093 chr19 59128983 2568407 0.04343736133597968 0.5734453391467155 chr20 63025520 2513420 0.03987940123302434 0.2454987048084137 chr21 48129895 1587612 0.032985985113825826 0.20956234732657505 chr22 51304566 1372598 0.02675391504140197 0.17253731939881822 chrMT 16571 19799 1.1947981413312414 1.33862761463872 chrX 155270560 7470452 0.048112481851034734 0.29806075400758386 chrY 59373566 335546 0.005651437543771584 0.11729744383941783