BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008745.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 = 2,971,117 number of mapped reads = 2,687,501 (90.45%) number of supplementary alignments = 15,719 (0.53%) number of secondary alignments = 0 number of mapped bases = 175,729,120 bp number of sequenced bases = 175,647,939 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,103 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9966 >>>>>>> ACTG content number of A's = 47,542,585 bp (27.07%) number of C's = 31,700,791 bp (18.05%) number of T's = 55,794,320 bp (31.76%) number of G's = 40,576,247 bp (23.1%) number of N's = 33,996 bp (0.02%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,259,245 number of insertions = 13,906 mapped reads with insertion percentage = 0.51% number of deletions = 49,311 mapped reads with deletion percentage = 1.82% homopolymer indels = 47.26% >>>>>>> Coverage mean coverageData = 0.0568X std coverageData = 0.6717X There is a 4.71% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 15401522 0.06179130843569694 0.9993735628340064 chr2 243199373 20392684 0.08385171289072361 0.49384763025288864 chr3 198022430 20493778 0.103492205403196 0.4381642398425904 chr4 191154276 11256414 0.05888654041932078 0.2927843541907718 chr5 180915260 3211150 0.017749470111034303 0.15675164166573524 chr6 171115067 12662635 0.07400070152793733 0.4166243363991646 chr7 159138663 13550988 0.08515207897655895 1.7225467223683322 chr8 146364022 5254896 0.035902921552675014 0.5453974310190909 chr9 141213431 5256376 0.03722291826476477 0.387184022322989 chr10 135534747 7614177 0.056178781962089766 1.4442636244182634 chr11 135006516 12194517 0.09032539584978254 0.473569185462421 chr12 133851895 6149555 0.04594298048600657 0.25440137650486766 chr13 115169878 3016797 0.026194323137166128 0.1845441304683744 chr14 107349540 8192192 0.07631324735997937 0.32779488276317265 chr15 102531392 8677042 0.08462814978655513 0.33378806290596963 chr16 90354753 2518586 0.027874416302150703 0.28266641559465633 chr17 81195210 2546395 0.03136139434826266 0.2221497881528506 chr18 78077248 2247917 0.028790935356737983 0.8439858823810642 chr19 59128983 2735799 0.04626832496002849 0.6069820011888625 chr20 63025520 2064265 0.03275284361001702 0.2239371811384605 chr21 48129895 1529433 0.031777193779458694 0.22433604724354378 chr22 51304566 1302671 0.025390936939219014 0.18141700242873546 chrMT 16571 109988 6.637378552893609 4.479916102199026 chrX 155270560 6956538 0.044802685067922725 0.3003673801511012 chrY 59373566 392805 0.006615822940464785 0.1668841439628599