BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617382.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 = 32,000,000 number of mapped reads = 29,303,628 (91.57%) number of supplementary alignments = 88,455 (0.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,916,864 number of mapped paired reads (second in pair) = 14,386,764 number of mapped paired reads (both in pair) = 28,430,410 number of mapped paired reads (singletons) = 873,218 number of mapped bases = 2,855,219,001 bp number of sequenced bases = 2,854,322,184 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,490,165 duplication rate = 1.5% >>>>>>> Insert size mean insert size = 66,998.9192 std insert size = 2,497,488.4573 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 53.1966 >>>>>>> ACTG content number of A's = 865,874,388 bp (30.34%) number of C's = 564,990,267 bp (19.79%) number of T's = 857,782,299 bp (30.05%) number of G's = 564,905,211 bp (19.79%) number of N's = 770,019 bp (0.03%) GC percentage = 39.59% >>>>>>> Mismatches and indels general error rate = 0.0154 number of mismatches = 43,125,039 number of insertions = 320,801 mapped reads with insertion percentage = 1.06% number of deletions = 375,130 mapped reads with deletion percentage = 1.24% homopolymer indels = 40.53% >>>>>>> Coverage mean coverageData = 0.9223X std coverageData = 9.0513X There is a 51.89% of reference with a coverageData >= 1X There is a 22.91% of reference with a coverageData >= 2X There is a 8.61% of reference with a coverageData >= 3X There is a 2.97% of reference with a coverageData >= 4X There is a 1.01% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% 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 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% 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 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% 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 185132888 0.7427579809319713 18.539609404578925 chr2 243199373 281730091 1.1584326370775635 8.057597440087727 chr3 198022430 228057560 1.1516753935400146 1.4424672782023902 chr4 191154276 156357638 0.8179656833834049 8.452088573310505 chr5 180915260 179725358 0.9934228765445214 1.4146204040413968 chr6 171115067 134324981 0.7849979744916326 3.4873187148518556 chr7 159138663 232374215 1.460199618492459 10.440371154738562 chr8 146364022 120320416 0.8220627880805298 6.941648841709558 chr9 141213431 120054661 0.8501646065097023 13.290408774924723 chr10 135534747 119447726 0.8813070348668597 18.619047701168068 chr11 135006516 152972148 1.1330723325976355 5.129946424416088 chr12 133851895 126173265 0.9426333859524365 1.334463706265822 chr13 115169878 125154863 1.0866978864039432 1.3009081199102088 chr14 107349540 82562278 0.7690976412195153 1.3504061191334271 chr15 102531392 64183388 0.6259876779981686 1.0395574303989281 chr16 90354753 71704521 0.7935888109837453 7.637638606322401 chr17 81195210 88383779 1.0885343975340418 6.606666790277548 chr18 78077248 51346364 0.6576354228058858 14.061783182624959 chr19 59128983 52519776 0.8882239019737579 9.0893989127139 chr20 63025520 81181174 1.288068293605511 2.3046384117653465 chr21 48129895 45460189 0.9445312315765493 3.0198982518990647 chr22 51304566 25181138 0.49081670430659136 0.8912767736882168 chrMT 16571 1977507 119.33540522599722 22.291015630797983 chrX 155270560 119337459 0.7685775011051676 2.8454111834899782 chrY 59373566 9555618 0.16094061118040306 7.567187861056681