BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472707.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,959,194 number of mapped reads = 16,802,825 (99.08%) number of supplementary alignments = 58,093 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,428,954 number of mapped paired reads (second in pair) = 8,373,871 number of mapped paired reads (both in pair) = 16,709,062 number of mapped paired reads (singletons) = 93,763 number of mapped bases = 1,654,015,968 bp number of sequenced bases = 1,653,792,773 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,402,175 duplication rate = 47.63% >>>>>>> Insert size mean insert size = 24,090.5116 std insert size = 1,547,673.6047 median insert size = 242 >>>>>>> Mapping quality mean mapping quality = 55.1843 >>>>>>> ACTG content number of A's = 458,853,286 bp (27.75%) number of C's = 370,525,508 bp (22.4%) number of T's = 456,378,830 bp (27.6%) number of G's = 367,713,698 bp (22.23%) number of N's = 321,451 bp (0.02%) GC percentage = 44.64% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 10,112,440 number of insertions = 95,839 mapped reads with insertion percentage = 0.56% number of deletions = 92,397 mapped reads with deletion percentage = 0.54% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.5343X std coverageData = 16.3403X There is a 4.85% of reference with a coverageData >= 1X There is a 2.11% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 156660624 0.6285265142829874 19.808632828071236 chr2 243199373 107713954 0.44290391324323025 14.3713440672159 chr3 198022430 182193072 0.9200628029865102 20.000367046620532 chr4 191154276 58087558 0.30387788971040336 9.790095154017337 chr5 180915260 75070668 0.4149493414762248 12.68931918949427 chr6 171115067 115011444 0.6721292637544303 17.00916225873199 chr7 159138663 75130298 0.4721058766215725 15.952164051463358 chr8 146364022 81433419 0.5563759309647831 19.100139740913818 chr9 141213431 103418893 0.7323587584243315 18.38760838246852 chr10 135534747 52581228 0.38795385806120997 14.012249642191149 chr11 135006516 85526438 0.6334985935049239 18.499355753636447 chr12 133851895 84484805 0.6311812395334411 22.549907722049614 chr13 115169878 44527737 0.3866265882473193 13.540589675150128 chr14 107349540 35400074 0.32976456163668705 10.272371918773391 chr15 102531392 44394819 0.43298757711199315 14.24795017938261 chr16 90354753 62622836 0.6930773857574487 18.070993284535803 chr17 81195210 66311668 0.8166943345549571 18.95484544068301 chr18 78077248 33430893 0.4281771432312778 16.77364617697902 chr19 59128983 33093492 0.5596830914544902 13.238356344600408 chr20 63025520 43170186 0.6849635830057411 20.07850148944259 chr21 48129895 6733607 0.13990487616895902 4.951185418011028 chr22 51304566 12026788 0.2344194471891644 5.148599345793881 chrMT 16571 4977 0.3003439744131314 0.9375589789537011 chrX 155270560 89818254 0.5784628715192371 17.090606442980835 chrY 59373566 5168236 0.08704607703704373 6.06466606011844