BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082899.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 = 3,118,636 number of mapped reads = 2,673,880 (85.74%) number of supplementary alignments = 20,133 (0.65%) number of secondary alignments = 0 number of mapped bases = 180,717,248 bp number of sequenced bases = 180,650,167 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 155,185 duplication rate = 4.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.257 >>>>>>> ACTG content number of A's = 51,137,236 bp (28.31%) number of C's = 32,578,905 bp (18.03%) number of T's = 59,136,954 bp (32.74%) number of G's = 37,787,004 bp (20.92%) number of N's = 10,068 bp (0.01%) GC percentage = 38.95% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,583,215 number of insertions = 14,420 mapped reads with insertion percentage = 0.54% number of deletions = 39,641 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.83% >>>>>>> Coverage mean coverageData = 0.0584X std coverageData = 0.505X There is a 4.57% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 16459138 0.06603449144465723 1.0168671184332956 chr2 243199373 18185167 0.07477472814043809 0.5523563552180157 chr3 198022430 12971468 0.06550504404980789 0.315324338288872 chr4 191154276 10213770 0.05343207703080626 0.2881201119804429 chr5 180915260 10353476 0.05722831783233764 0.2924175879160585 chr6 171115067 13054164 0.07628880512316312 0.5315424295884732 chr7 159138663 8925942 0.05608908502643383 0.38850011001998536 chr8 146364022 16131133 0.1102124195521219 0.7321602678687187 chr9 141213431 5178426 0.03667091694698644 0.3967542795710656 chr10 135534747 6618631 0.048833462610145276 0.4564042720653908 chr11 135006516 7450073 0.05518306242344629 0.3577791116638441 chr12 133851895 5537415 0.04136971687998889 0.25788100549128956 chr13 115169878 4424345 0.03841581737196943 0.23756024531534367 chr14 107349540 4083579 0.03804002327350448 0.28365322466042764 chr15 102531392 3463586 0.033780737122929144 0.22113442468362032 chr16 90354753 6618862 0.07325416516826735 0.3737775385730726 chr17 81195210 4142548 0.05101961063959315 0.3289154449784263 chr18 78077248 6411790 0.08212110652260694 1.0052619989502354 chr19 59128983 2943971 0.04978896728191655 0.6481039180130274 chr20 63025520 3403449 0.05400112525846673 0.3040806068957048 chr21 48129895 4355159 0.0904876065073485 0.37401222514220295 chr22 51304566 2154334 0.04199107736336762 0.244623189487363 chrMT 16571 151266 9.128356767847444 5.740178618885768 chrX 155270560 7188981 0.0462997042066442 0.3046975277526345 chrY 59373566 296575 0.004995068007200376 0.10349980495671401