BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013323.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 = 2,209,853 number of mapped reads = 1,917,736 (86.78%) number of supplementary alignments = 11,936 (0.54%) number of secondary alignments = 0 number of mapped bases = 128,050,303 bp number of sequenced bases = 127,996,470 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,300 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3033 >>>>>>> ACTG content number of A's = 35,636,589 bp (27.84%) number of C's = 23,466,219 bp (18.33%) number of T's = 40,663,514 bp (31.77%) number of G's = 28,228,349 bp (22.05%) number of N's = 1,799 bp (0%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 922,643 number of insertions = 9,197 mapped reads with insertion percentage = 0.48% number of deletions = 31,215 mapped reads with deletion percentage = 1.61% homopolymer indels = 47.29% >>>>>>> Coverage mean coverageData = 0.0414X std coverageData = 0.4069X There is a 3.5% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% 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 11787508 0.04729178989688455 0.8345062103704823 chr2 243199373 7460735 0.03067744339949429 0.4467598907687686 chr3 198022430 5196517 0.02624206257846649 0.1865179145332783 chr4 191154276 7561501 0.03955705913688271 0.2421081049174197 chr5 180915260 8957913 0.0495144135436668 0.2572973413284668 chr6 171115067 9506804 0.05555795972075329 0.365118687485187 chr7 159138663 5604739 0.0352192163383954 0.2891113479374525 chr8 146364022 7040352 0.048101657113522066 0.46130893702081577 chr9 141213431 5585964 0.03955688889111405 0.4065138501245683 chr10 135534747 5875636 0.04335151044329614 0.3635017949720414 chr11 135006516 5802938 0.04298265129662334 0.3388581257419829 chr12 133851895 4668402 0.03487736949857901 0.2204622875304837 chr13 115169878 3320327 0.02882982128365196 0.19250313913087602 chr14 107349540 4894656 0.04559550045580074 0.2654742004329118 chr15 102531392 3822645 0.03728267924032476 0.22540494039694553 chr16 90354753 5537743 0.06128889533901996 0.3133403074731514 chr17 81195210 2593797 0.031945197259789095 0.23533825165259825 chr18 78077248 3409225 0.04366476902464595 0.7972551649863263 chr19 59128983 2828970 0.04784404967695791 0.6288434089744621 chr20 63025520 3354081 0.05321782351022253 0.2743065101712769 chr21 48129895 2265197 0.0470642414657252 0.2683800385400723 chr22 51304566 1394880 0.02718822336397895 0.18466681111279343 chrMT 16571 8384 0.5059441192444633 0.8492790952981526 chrX 155270560 9223123 0.05940033319903013 0.3110466385661366 chrY 59373566 348266 0.005865674296874808 0.12817328535617167