BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617390.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 26,236,032 number of mapped reads = 23,862,638 (90.95%) number of supplementary alignments = 67,145 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,066,247 number of mapped paired reads (second in pair) = 11,796,391 number of mapped paired reads (both in pair) = 23,243,762 number of mapped paired reads (singletons) = 618,876 number of mapped bases = 2,322,546,264 bp number of sequenced bases = 2,321,882,504 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,175,667 duplication rate = 1.4% >>>>>>> Insert size mean insert size = 54,229.4446 std insert size = 2,225,307.6915 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 53.2803 >>>>>>> ACTG content number of A's = 706,730,604 bp (30.44%) number of C's = 457,906,078 bp (19.72%) number of T's = 696,980,351 bp (30.02%) number of G's = 459,658,406 bp (19.8%) number of N's = 607,065 bp (0.03%) GC percentage = 39.52% >>>>>>> Mismatches and indels general error rate = 0.0152 number of mismatches = 34,585,977 number of insertions = 235,901 mapped reads with insertion percentage = 0.96% number of deletions = 281,131 mapped reads with deletion percentage = 1.14% homopolymer indels = 40.84% >>>>>>> Coverage mean coverageData = 0.7503X std coverageData = 7.6793X There is a 45.21% of reference with a coverageData >= 1X There is a 17.68% of reference with a coverageData >= 2X There is a 5.91% of reference with a coverageData >= 3X There is a 1.84% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 150405695 0.6034315758033758 15.813422566409995 chr2 243199373 229670577 0.944371583556673 6.768387463117557 chr3 198022430 185847728 0.9385185708507869 1.286883678778785 chr4 191154276 127914713 0.6691700320635254 6.845306518249665 chr5 180915260 146466264 0.8095849073206981 1.2489902943721563 chr6 171115067 109330081 0.6389272605667156 2.9399110861563362 chr7 159138663 188859965 1.186763552236203 8.786847595802168 chr8 146364022 98096327 0.6702215862857335 6.007857661770762 chr9 141213431 97600453 0.6911555955325525 11.311033853413836 chr10 135534747 97802371 0.7216036711235385 16.049035698415775 chr11 135006516 124277573 0.9205301838912723 4.408554363852393 chr12 133851895 102777325 0.7678436304543914 1.179421267032583 chr13 115169878 101775750 0.8837011184469605 1.1403759930039754 chr14 107349540 67186650 0.6258680754477383 1.1754221852980753 chr15 102531392 52034533 0.5074985522482715 0.9142101218719536 chr16 90354753 57985067 0.641748940423754 6.384229724096473 chr17 81195210 71164009 0.8764557539785907 5.606362523594083 chr18 78077248 41847200 0.5359717596603815 11.690768807911105 chr19 59128983 42143264 0.7127344639091797 7.559618592169564 chr20 63025520 65733769 1.0429706728322115 1.9576726499998225 chr21 48129895 36931627 0.7673323825036393 2.5733984940069448 chr22 51304566 20195628 0.3936419226312138 0.7850576264954722 chrMT 16571 1545962 93.29322310059743 17.75604084199047 chrX 155270560 97163847 0.6257712150970538 2.386899983463275 chrY 59373566 7789886 0.1312012487173164 6.197069144497957