BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081995.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 = 1,737,357 number of mapped reads = 1,544,683 (88.91%) number of supplementary alignments = 22,250 (1.28%) number of secondary alignments = 0 number of mapped bases = 106,048,738 bp number of sequenced bases = 106,010,153 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,237 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4632 >>>>>>> ACTG content number of A's = 30,437,750 bp (28.71%) number of C's = 20,375,002 bp (19.22%) number of T's = 31,473,252 bp (29.69%) number of G's = 23,710,803 bp (22.37%) number of N's = 13,346 bp (0.01%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 911,519 number of insertions = 9,583 mapped reads with insertion percentage = 0.61% number of deletions = 21,485 mapped reads with deletion percentage = 1.37% homopolymer indels = 44.06% >>>>>>> Coverage mean coverageData = 0.0343X std coverageData = 0.5047X There is a 3.07% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% 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 9721672 0.03900360192081528 0.9631125554740085 chr2 243199373 9311327 0.03828680512264314 0.7456241197651661 chr3 198022430 6413258 0.032386523082258915 0.1987441556355496 chr4 191154276 5308519 0.02777086189795723 0.21900963418203426 chr5 180915260 5366834 0.029664904994747266 0.1899272103111316 chr6 171115067 8529885 0.04984882482616215 0.3405537457773591 chr7 159138663 6870000 0.043169898945299046 0.7278301669490843 chr8 146364022 5779099 0.03948442329632073 0.5309723758119955 chr9 141213431 5355190 0.037922667568356154 0.5537198313826285 chr10 135534747 4505640 0.03324343092624064 0.516862022942379 chr11 135006516 4821976 0.03571661681870229 0.3458152260924809 chr12 133851895 4463760 0.033348500594631104 0.2132209760091829 chr13 115169878 2659408 0.023091176670344306 0.15853090431738473 chr14 107349540 2683804 0.025000610156317393 0.24060308470324795 chr15 102531392 2482678 0.02421383296932124 0.1708133428958606 chr16 90354753 2510727 0.02778743692653335 0.27108086573323 chr17 81195210 3264502 0.040205598335172725 0.26521925226862264 chr18 78077248 3073444 0.03936414357227345 0.9984153809314157 chr19 59128983 2526119 0.04272217907079511 0.6841031718362819 chr20 63025520 2661028 0.04222143664978885 0.23830476812996199 chr21 48129895 1144478 0.023778942380821733 0.2366858805623503 chr22 51304566 958948 0.01869127983657439 0.14284664617375575 chrMT 16571 41449 2.5012974473477763 2.329332053493997 chrX 155270560 5287688 0.034054672051160244 0.27930811525303084 chrY 59373566 307305 0.005175788161351131 0.17618260971907476