BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777299.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 1,481,956 number of mapped reads = 1,452,322 (98%) number of supplementary alignments = 57,615 (3.89%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 727,693 number of mapped paired reads (second in pair) = 724,629 number of mapped paired reads (both in pair) = 1,444,494 number of mapped paired reads (singletons) = 7,828 number of mapped bases = 140,003,503 bp number of sequenced bases = 139,941,504 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 137,835 duplication rate = 7.72% >>>>>>> Insert size mean insert size = 165,660.9744 std insert size = 3,872,185.0572 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 52.7904 >>>>>>> ACTG content number of A's = 41,661,017 bp (29.77%) number of C's = 28,454,199 bp (20.33%) number of T's = 40,867,121 bp (29.2%) number of G's = 28,956,908 bp (20.69%) number of N's = 2,259 bp (0%) GC percentage = 41.03% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 938,521 number of insertions = 35,184 mapped reads with insertion percentage = 2.34% number of deletions = 22,004 mapped reads with deletion percentage = 1.45% homopolymer indels = 41.99% >>>>>>> Coverage mean coverageData = 0.0452X std coverageData = 0.6721X There is a 3.14% of reference with a coverageData >= 1X There is a 0.96% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 11267960 0.04520734975420583 1.151544216425727 chr2 243199373 12659460 0.052053834859187735 0.630641045362703 chr3 198022430 9559990 0.04827730878769643 0.3409024938597504 chr4 191154276 9734137 0.05092293619421833 0.6094779940363632 chr5 180915260 8605515 0.04756655132353125 0.2807141649620296 chr6 171115067 8118276 0.04744337329453285 0.334945153152739 chr7 159138663 7424847 0.046656462106885996 0.4711256929550847 chr8 146364022 7168123 0.048974624378660486 0.4241784795543077 chr9 141213431 5880843 0.04164506844961511 0.5770430738463561 chr10 135534747 7882092 0.05815550753195415 1.849720164641982 chr11 135006516 6388449 0.0473195604869916 0.3271182700686348 chr12 133851895 6213524 0.04642088929708466 0.28233051473313553 chr13 115169878 4637479 0.04026642278808353 0.2594301328636968 chr14 107349540 4109088 0.03827764888419643 0.26029656133084844 chr15 102531392 3778910 0.03685612695085618 0.2416032718165786 chr16 90354753 4825792 0.05340938732907609 0.908156485466849 chr17 81195210 3244945 0.03996473437287742 0.3620764555203586 chr18 78077248 3923433 0.050250656887906704 0.6807572805977954 chr19 59128983 2106416 0.0356240864146099 0.6694655549734578 chr20 63025520 2642646 0.041929777017309815 0.29309818203325577 chr21 48129895 1891629 0.03930257898962796 0.3243482286781006 chr22 51304566 1260255 0.024564187912631402 0.21406069999450525 chrMT 16571 559379 33.75650232333595 10.844426357217808 chrX 155270560 4103145 0.026425775755558555 0.23032500522711236 chrY 59373566 2017170 0.03397421000449931 0.7691218375535694