BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080816.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 = 2,619,551 number of mapped reads = 2,418,830 (92.34%) number of supplementary alignments = 18,788 (0.72%) number of secondary alignments = 0 number of mapped bases = 166,571,857 bp number of sequenced bases = 166,506,847 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 136,028 duplication rate = 4.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8864 >>>>>>> ACTG content number of A's = 47,759,283 bp (28.68%) number of C's = 31,134,106 bp (18.7%) number of T's = 52,526,682 bp (31.55%) number of G's = 35,062,827 bp (21.06%) number of N's = 23,949 bp (0.01%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,347,541 number of insertions = 12,399 mapped reads with insertion percentage = 0.51% number of deletions = 36,687 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.72% >>>>>>> Coverage mean coverageData = 0.0538X std coverageData = 0.4378X There is a 4.26% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 21537318 0.08640828220845236 0.9180432179155448 chr2 243199373 12092216 0.04972141108274979 0.3884426847303562 chr3 198022430 9718983 0.04908021278195607 0.2749039380531582 chr4 191154276 10841148 0.056714127598171016 0.31388084725459325 chr5 180915260 11578483 0.0639994824096099 0.3039298390460412 chr6 171115067 10360304 0.060545831419976597 0.3834747331442808 chr7 159138663 12409610 0.07797985584433369 0.49507238116787944 chr8 146364022 7937267 0.05422963165087114 0.5927308171843872 chr9 141213431 6172410 0.04370979414840505 0.30333434511534685 chr10 135534747 7750177 0.057182214683294465 0.5319416886544155 chr11 135006516 6278383 0.0465042961333807 0.2809421617046435 chr12 133851895 5525089 0.04127763002533509 0.2484323308647669 chr13 115169878 6916064 0.06005097964938367 0.2943214234477086 chr14 107349540 4142143 0.03858556822879725 0.2531052267072368 chr15 102531392 4393899 0.042854182648763804 0.2478128267867262 chr16 90354753 4104900 0.0454309249232301 0.2965056287942967 chr17 81195210 4382518 0.053975080549702376 0.2910475285560627 chr18 78077248 2285436 0.02927147227320307 0.512571428630424 chr19 59128983 2348447 0.03971735823699183 0.6366929917091588 chr20 63025520 2853287 0.04527193111615739 0.2660350976629355 chr21 48129895 2963181 0.0615663300325089 0.31698993794158636 chr22 51304566 668561 0.013031218313005513 0.13523243922617934 chrMT 16571 26247 1.5839116528875747 1.7475883183668708 chrX 155270560 8841186 0.05694051724937425 0.3013319045864143 chrY 59373566 444600 0.007488180851391004 0.20860674996233008