BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472753.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 = 15,394,096 number of mapped reads = 15,250,073 (99.06%) number of supplementary alignments = 56,019 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,661,119 number of mapped paired reads (second in pair) = 7,588,954 number of mapped paired reads (both in pair) = 15,151,280 number of mapped paired reads (singletons) = 98,793 number of mapped bases = 1,505,463,909 bp number of sequenced bases = 1,505,240,345 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,236,331 duplication rate = 46.72% >>>>>>> Insert size mean insert size = 23,904.3413 std insert size = 1,517,700.5117 median insert size = 268 >>>>>>> Mapping quality mean mapping quality = 55.4083 >>>>>>> ACTG content number of A's = 422,358,594 bp (28.06%) number of C's = 332,330,293 bp (22.08%) number of T's = 419,118,643 bp (27.84%) number of G's = 331,145,981 bp (22%) number of N's = 286,834 bp (0.02%) GC percentage = 44.08% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 9,988,635 number of insertions = 95,653 mapped reads with insertion percentage = 0.62% number of deletions = 94,686 mapped reads with deletion percentage = 0.61% homopolymer indels = 46.03% >>>>>>> Coverage mean coverageData = 0.4863X std coverageData = 15.5X There is a 4.38% of reference with a coverageData >= 1X There is a 1.84% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.51% 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 0.32% of reference with a coverageData >= 13X There is a 0.31% 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 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 161457316 0.6477709678404372 18.78337586952941 chr2 243199373 83436300 0.3430777759447595 10.372775495925763 chr3 198022430 187645580 0.9475976029584123 20.879496970023002 chr4 191154276 55584470 0.29078329380400575 11.892013596693511 chr5 180915260 77494728 0.4283482112011999 19.44838809939967 chr6 171115067 103286890 0.6036107270436916 16.350913591407565 chr7 159138663 54963908 0.3453837487625493 9.21133126121319 chr8 146364022 80502129 0.5500130967977909 16.229768835474356 chr9 141213431 89061275 0.6306855825916445 16.260458156505123 chr10 135534747 36286503 0.2677284150609733 8.954288942336508 chr11 135006516 69582723 0.5154027010074091 15.572292960500889 chr12 133851895 84484263 0.6311771902818409 19.741138941858726 chr13 115169878 35271515 0.30625642409728004 10.275192790825104 chr14 107349540 34994595 0.32598737730967453 11.783443071503864 chr15 102531392 38639771 0.3768579578047668 12.213520418389853 chr16 90354753 52492675 0.580961966660459 18.862659186186075 chr17 81195210 65222661 0.8032821271107002 17.819852044756036 chr18 78077248 21071612 0.26988159213808355 9.626475844362393 chr19 59128983 34279184 0.5797357279085961 18.04730371541016 chr20 63025520 30003723 0.47605673067036974 12.169804695586405 chr21 48129895 5733538 0.1191263350979677 4.5827844025323605 chr22 51304566 13239036 0.25804790941999195 8.607234618783428 chrMT 16571 1543 0.09311447709854566 0.33054163894494 chrX 155270560 89015307 0.5732915950068062 22.09644232602192 chrY 59373566 1712664 0.02884556403433811 1.0270559642581838