BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046424.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 7,137,388 number of mapped reads = 7,109,081 (99.6%) number of supplementary alignments = 42,024 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,558,843 number of mapped paired reads (second in pair) = 3,550,238 number of mapped paired reads (both in pair) = 7,088,994 number of mapped paired reads (singletons) = 20,087 number of mapped bases = 688,166,850 bp number of sequenced bases = 687,985,404 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,404,790 duplication rate = 36.35% >>>>>>> Insert size mean insert size = 53,547.3983 std insert size = 2,431,949.5138 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 52.4615 >>>>>>> ACTG content number of A's = 202,132,659 bp (29.38%) number of C's = 142,084,878 bp (20.65%) number of T's = 200,597,496 bp (29.16%) number of G's = 143,111,540 bp (20.8%) number of N's = 58,831 bp (0.01%) GC percentage = 41.45% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 2,497,031 number of insertions = 57,830 mapped reads with insertion percentage = 0.8% number of deletions = 66,653 mapped reads with deletion percentage = 0.91% homopolymer indels = 49.74% >>>>>>> Coverage mean coverageData = 0.2223X std coverageData = 23.4135X There is a 2.17% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 217162781 0.8712627480274161 53.72632982636553 chr2 243199373 26325809 0.10824784897780143 9.497177103617114 chr3 198022430 35319777 0.17836250671199216 14.610693618732823 chr4 191154276 11537015 0.060354469915179926 6.621935223524265 chr5 180915260 31212719 0.17252673433960186 18.749587313695883 chr6 171115067 63145641 0.3690244354694961 32.305774212306005 chr7 159138663 44665029 0.28066736365631023 26.800863058207213 chr8 146364022 75502064 0.5158512520242167 31.816148287315972 chr9 141213431 11558011 0.08184781658622826 22.75760566849066 chr10 135534747 43836429 0.3234331414659298 36.06417916242827 chr11 135006516 10784185 0.07987899635896092 4.540367355626899 chr12 133851895 5828741 0.0435461970859658 1.715094343207238 chr13 115169878 12687291 0.11016153893989537 9.495538341138207 chr14 107349540 9442663 0.08796183942660583 8.61232532451715 chr15 102531392 10768903 0.10503030135395021 8.344069269075518 chr16 90354753 30077982 0.332887656723493 26.973297648244717 chr17 81195210 6280104 0.07734574490293208 5.371165268840683 chr18 78077248 2761119 0.03536393854455526 2.0555282978552434 chr19 59128983 1663353 0.028130925235091562 1.3777108407454401 chr20 63025520 3088898 0.04901027393347965 2.844913405711483 chr21 48129895 1611172 0.03347549376536142 1.7606326679095448 chr22 51304566 10462847 0.20393598105868393 15.931807290099597 chrMT 16571 71255 4.299981896083519 3.3273860306596648 chrX 155270560 22285002 0.14352367892535456 16.02480444284744 chrY 59373566 88060 0.0014831516099268823 0.08979970677479135