BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124894.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,308,442 number of mapped reads = 4,254,865 (98.76%) number of supplementary alignments = 17,926 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,128,785 number of mapped paired reads (second in pair) = 2,126,080 number of mapped paired reads (both in pair) = 4,240,516 number of mapped paired reads (singletons) = 14,349 number of mapped bases = 389,543,233 bp number of sequenced bases = 389,336,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 213,493 duplication rate = 2.75% >>>>>>> Insert size mean insert size = 55,085.5913 std insert size = 2,199,903.3654 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 52.5074 >>>>>>> ACTG content number of A's = 114,386,951 bp (29.38%) number of C's = 77,568,282 bp (19.92%) number of T's = 114,507,173 bp (29.41%) number of G's = 82,619,772 bp (21.22%) number of N's = 254,459 bp (0.07%) GC percentage = 41.14% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 3,289,828 number of insertions = 64,830 mapped reads with insertion percentage = 1.49% number of deletions = 120,757 mapped reads with deletion percentage = 2.78% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 0.1258X std coverageData = 1.3076X There is a 8.62% of reference with a coverageData >= 1X There is a 2.55% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 30165893 0.12102635042181098 1.319767990407263 chr2 243199373 31808441 0.1307916242037351 1.509337293703982 chr3 198022430 28792988 0.14540265968860194 0.5089487267954957 chr4 191154276 17881333 0.09354398642905587 1.21456297089655 chr5 180915260 17910967 0.09900196920923089 0.4111780864646945 chr6 171115067 24314657 0.14209535972656342 0.7655713485858426 chr7 159138663 18107564 0.11378481921769068 2.2693462748320488 chr8 146364022 24483230 0.1672762859714254 0.717538984242002 chr9 141213431 22031648 0.15601666104975526 1.8674419856303286 chr10 135534747 24129440 0.17803139441430468 3.00794367468855 chr11 135006516 16950758 0.12555511024371593 0.627304261258211 chr12 133851895 15039467 0.11235901441664312 0.4290194899224436 chr13 115169878 13052283 0.11333070093206142 0.4297619569653439 chr14 107349540 12347877 0.11502496424297673 0.48133008330363436 chr15 102531392 8968659 0.08747232262290948 0.38071800096111297 chr16 90354753 12734229 0.14093590627158264 2.251691662316205 chr17 81195210 11064552 0.1362709943111176 1.0614782785670924 chr18 78077248 8945096 0.11456725523932401 1.9782740795725873 chr19 59128983 5382375 0.09102769448951963 0.8308990701364195 chr20 63025520 11175591 0.17731850526580345 0.6196582052059119 chr21 48129895 7213213 0.14986970156490056 0.6830914319125692 chr22 51304566 4938534 0.0962591516708279 0.40923378922145115 chrMT 16571 90237 5.445477038199264 4.298394138503537 chrX 155270560 20998156 0.13523591336309987 0.590805124703067 chrY 59373566 1016045 0.017112750142041326 1.1571383163843263