BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617373.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 = 1,678,552 number of mapped reads = 1,473,369 (87.78%) number of supplementary alignments = 3,953 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 751,382 number of mapped paired reads (second in pair) = 721,987 number of mapped paired reads (both in pair) = 1,425,374 number of mapped paired reads (singletons) = 47,995 number of mapped bases = 143,754,941 bp number of sequenced bases = 143,714,312 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,118 duplication rate = 0.96% >>>>>>> Insert size mean insert size = 43,118.9636 std insert size = 1,958,603.9673 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 53.2045 >>>>>>> ACTG content number of A's = 43,703,842 bp (30.41%) number of C's = 28,398,751 bp (19.76%) number of T's = 42,932,101 bp (29.87%) number of G's = 28,638,734 bp (19.93%) number of N's = 40,884 bp (0.03%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0171 number of mismatches = 2,422,176 number of insertions = 14,409 mapped reads with insertion percentage = 0.95% number of deletions = 17,245 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.1% >>>>>>> Coverage mean coverageData = 0.0464X std coverageData = 0.5281X There is a 3.99% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.03% 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 0.01% 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 9388282 0.03766603253518073 1.0188499080647464 chr2 243199373 14069048 0.05784985309152092 0.4822424889268814 chr3 198022430 11492034 0.05803400150174907 0.2632942705826226 chr4 191154276 7913682 0.041399450567352204 0.48644457590010176 chr5 180915260 9054850 0.050050227935443364 0.24540963047445544 chr6 171115067 6809209 0.03979315860011322 0.27481823601887373 chr7 159138663 11673043 0.07335139544310486 0.6153015183596339 chr8 146364022 6172511 0.042172324288820104 0.42025345292250327 chr9 141213431 5988852 0.04240993195611825 0.7134523392688451 chr10 135534747 6046046 0.04460882639932917 1.0341463671261206 chr11 135006516 7684704 0.05692098594707829 0.35010848990596205 chr12 133851895 6409649 0.047886128171737874 0.2393511259934218 chr13 115169878 6296351 0.05467011956025516 0.25370494421757384 chr14 107349540 4174089 0.038883156835138745 0.21672976726891033 chr15 102531392 3227416 0.03147734500668829 0.1930150578982142 chr16 90354753 3638679 0.040271030346350455 0.47278117835208894 chr17 81195210 4433148 0.054598639501024754 0.43871426054582024 chr18 78077248 2529717 0.03240018142032875 0.736508062235364 chr19 59128983 2573123 0.04351711917656355 0.48323785276767117 chr20 63025520 4071181 0.0645957542278112 0.29006999890953167 chr21 48129895 2272926 0.04722482772921071 0.2769963680501608 chr22 51304566 1221614 0.023811019081615464 0.16726148969810717 chrMT 16571 87889 5.303783718544445 2.526833458501028 chrX 155270560 6046631 0.03894254648144503 0.25565412426847073 chrY 59373566 480267 0.00808890272819389 0.37756995406034866