BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006193.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 4,531,984 number of mapped reads = 3,930,283 (86.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,968,231 number of mapped paired reads (second in pair) = 1,962,052 number of mapped paired reads (both in pair) = 3,645,286 number of mapped paired reads (singletons) = 284,997 number of mapped bases = 152,062,275 bp number of sequenced bases = 152,042,673 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,326 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 53,273.604 std insert size = 2,205,203.4335 median insert size = 110 >>>>>>> Mapping quality mean mapping quality = 47.7845 >>>>>>> ACTG content number of A's = 41,692,744 bp (27.42%) number of C's = 33,285,218 bp (21.89%) number of T's = 42,594,922 bp (28.02%) number of G's = 34,462,629 bp (22.67%) number of N's = 7,160 bp (0%) GC percentage = 44.56% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 444,726 number of insertions = 4,779 mapped reads with insertion percentage = 0.12% number of deletions = 14,829 mapped reads with deletion percentage = 0.38% homopolymer indels = 44.4% >>>>>>> Coverage mean coverageData = 0.0491X std coverageData = 0.3135X There is a 4.11% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.09% 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 12775486 0.05125558343142503 0.3908850038626841 chr2 243199373 12580079 0.051727431879522154 0.30954949716163566 chr3 198022430 10850370 0.054793641306189404 0.2684483912747285 chr4 191154276 9373685 0.0490372760481696 0.2741313202071762 chr5 180915260 8853553 0.04893756889275123 0.25425215191370937 chr6 171115067 8320227 0.0486235791264366 0.2720935361338684 chr7 159138663 8098179 0.05088756463914743 0.35045534345549273 chr8 146364022 7600715 0.05193021410685202 0.4751565136147996 chr9 141213431 6325543 0.04479420233051345 0.2740886853641817 chr10 135534747 7096592 0.05235994574881967 0.31736349591251795 chr11 135006516 6965057 0.051590524712155375 0.2905406043283692 chr12 133851895 6948089 0.051908783211474144 0.266066333768166 chr13 115169878 4697249 0.04078539529233503 0.23102878801013732 chr14 107349540 4646764 0.04328629633624886 0.4570522712769496 chr15 102531392 4352153 0.042447029296159365 0.23688866653670484 chr16 90354753 4719625 0.052234385500450654 0.28961075798848035 chr17 81195210 4487505 0.05526810017487485 0.28067137660875996 chr18 78077248 3761945 0.04818234628351655 0.3858448466919934 chr19 59128983 3310911 0.055994722588074954 0.34481333321016594 chr20 63025520 3544182 0.05623407787829438 0.28071043429472764 chr21 48129895 1955836 0.040636614727707174 0.2577158783301394 chr22 51304566 2074881 0.04044242377959108 0.25657379341919884 chrMT 16571 19727 1.1904532013758977 1.321031495575612 chrX 155270560 8339427 0.05370900317484525 0.2800357163472223 chrY 59373566 364495 0.0061390114247138194 0.14699139212739457