BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708553.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,989,161 number of mapped reads = 3,289,035 (82.45%) number of supplementary alignments = 92 (0%) number of secondary alignments = 0 number of mapped bases = 164,007,777 bp number of sequenced bases = 163,992,563 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,505 duplication rate = 0.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3638 >>>>>>> ACTG content number of A's = 50,842,443 bp (31%) number of C's = 31,122,406 bp (18.98%) number of T's = 50,642,082 bp (30.88%) number of G's = 31,378,593 bp (19.13%) number of N's = 7,039 bp (0%) GC percentage = 38.11% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 264,369 number of insertions = 11,305 mapped reads with insertion percentage = 0.34% number of deletions = 8,857 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.84% >>>>>>> Coverage mean coverageData = 0.053X std coverageData = 0.2382X There is a 4.99% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 12679697 0.05087127546213817 0.2345235700701529 chr2 243199373 13979592 0.05748202319584105 0.24728262758086164 chr3 198022430 12673090 0.06399825514715682 0.2603948106535565 chr4 191154276 11906073 0.062285151287957585 0.2572803720047255 chr5 180915260 11498306 0.06355630807484122 0.2594409025633869 chr6 171115067 9573484 0.05594763902351159 0.24398381934543267 chr7 159138663 8987528 0.05647608086288874 0.2460157596768344 chr8 146364022 8523687 0.0582362173676807 0.24883107784951455 chr9 141213431 6935373 0.04911270090165857 0.23000142592112208 chr10 135534747 6967828 0.051409901550928484 0.23325706104719615 chr11 135006516 7205866 0.053374208990031265 0.23889149534093512 chr12 133851895 7422169 0.0554506083010629 0.24384587823401244 chr13 115169878 6440838 0.05592467502657249 0.2447263352926794 chr14 107349540 6632206 0.06178141052118155 0.258531743390521 chr15 102531392 4622359 0.045082378282740955 0.22026161866731234 chr16 90354753 3253390 0.03600684957879305 0.19591411649082835 chr17 81195210 2812917 0.03464387862288921 0.19242322563353348 chr18 78077248 4022538 0.05151997672868798 0.23336601105162305 chr19 59128983 1484631 0.025108346612354216 0.1625359825993601 chr20 63025520 2399590 0.038073307447522846 0.20199205858350017 chr21 48129895 2078997 0.043195544058427716 0.21738488198478856 chr22 51304566 1035858 0.02019036668198304 0.14654388499828871 chrMT 16571 100 0.006034638826866212 0.07744818888195831 chrX 155270560 10639713 0.06852369824646733 0.27167881669592886 chrY 59373566 231947 0.003906570139310817 0.06554084048664606