BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006072.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 = 6,395,092 number of mapped reads = 5,572,875 (87.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,832,042 number of mapped paired reads (second in pair) = 2,740,833 number of mapped paired reads (both in pair) = 5,075,706 number of mapped paired reads (singletons) = 497,169 number of mapped bases = 215,184,531 bp number of sequenced bases = 215,159,167 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 241,532 duplication rate = 3.89% >>>>>>> Insert size mean insert size = 66,671.6853 std insert size = 2,579,167.0478 median insert size = 105 >>>>>>> Mapping quality mean mapping quality = 47.0134 >>>>>>> ACTG content number of A's = 57,546,027 bp (26.75%) number of C's = 47,651,108 bp (22.15%) number of T's = 59,352,209 bp (27.59%) number of G's = 50,601,087 bp (23.52%) number of N's = 8,736 bp (0%) GC percentage = 45.66% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 1,017,006 number of insertions = 7,176 mapped reads with insertion percentage = 0.13% number of deletions = 19,683 mapped reads with deletion percentage = 0.35% homopolymer indels = 45.53% >>>>>>> Coverage mean coverageData = 0.0695X std coverageData = 0.4038X There is a 4.81% of reference with a coverageData >= 1X There is a 1.44% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 18292206 0.07338880812658036 0.4205538449878896 chr2 243199373 18603157 0.0764934414530748 0.44277271106274646 chr3 198022430 14634861 0.0739050672189004 0.36894021119942855 chr4 191154276 13033119 0.06818115332141458 0.3661406421665529 chr5 180915260 12772577 0.07059977693423981 0.35887617359926544 chr6 171115067 12284145 0.07178879811910427 0.39795316169752376 chr7 159138663 11875506 0.07462363812871797 0.5037577246303124 chr8 146364022 10782585 0.07366964130023702 0.42843892444523746 chr9 141213431 9198168 0.06513663703844148 0.3735443539299225 chr10 135534747 10522546 0.07763725710868816 0.3958549950808698 chr11 135006516 10015223 0.0741832564585253 0.5849329245977165 chr12 133851895 9932936 0.07420840773303956 0.3732772328961929 chr13 115169878 6580848 0.057140357481319896 0.32446544670429806 chr14 107349540 6716753 0.0625689965695242 0.3485640331598668 chr15 102531392 6691288 0.06526087151923189 0.350826336079984 chr16 90354753 7034452 0.0778537018412302 0.41568706375302217 chr17 81195210 6680121 0.08227235325827718 0.42916863319043497 chr18 78077248 5550093 0.07108463915121599 0.4481539405600209 chr19 59128983 5059465 0.08556658246599641 0.4818723378983555 chr20 63025520 5216842 0.08277348604184463 0.4011114166742312 chr21 48129895 2848954 0.05919302337975182 0.3611902438360678 chr22 51304566 3112978 0.060676431801411204 0.3671252823967913 chrMT 16571 21160 1.2769295757648904 1.8028756228575398 chrX 155270560 6358982 0.04095420277997323 0.2810839786844374 chrY 59373566 1365566 0.022999561791521836 0.22853278153909254