BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504618.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 302,651,498 number of mapped reads = 287,251,568 (94.91%) number of supplementary alignments = 3,135,834 (1.04%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 144,090,977 number of mapped paired reads (second in pair) = 143,160,591 number of mapped paired reads (both in pair) = 282,970,128 number of mapped paired reads (singletons) = 4,281,440 number of mapped bases = 27,687,249,625 bp number of sequenced bases = 27,661,338,998 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,819,244 duplication rate = 18.4% >>>>>>> Insert size mean insert size = 116,331.0589 std insert size = 3,216,948.4497 median insert size = 337 >>>>>>> Mapping quality mean mapping quality = 52.3438 >>>>>>> ACTG content number of A's = 7,376,283,622 bp (26.67%) number of C's = 6,408,797,511 bp (23.17%) number of T's = 7,453,723,733 bp (26.95%) number of G's = 6,417,848,775 bp (23.2%) number of N's = 4,685,357 bp (0.02%) GC percentage = 46.37% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 276,700,699 number of insertions = 8,440,075 mapped reads with insertion percentage = 2.72% number of deletions = 7,863,071 mapped reads with deletion percentage = 2.55% homopolymer indels = 34.59% >>>>>>> Coverage mean coverageData = 8.9438X std coverageData = 221.3076X There is a 83.19% of reference with a coverageData >= 1X There is a 74.44% of reference with a coverageData >= 2X There is a 66.13% of reference with a coverageData >= 3X There is a 58.75% of reference with a coverageData >= 4X There is a 52.23% of reference with a coverageData >= 5X There is a 46.51% of reference with a coverageData >= 6X There is a 41.45% of reference with a coverageData >= 7X There is a 36.98% of reference with a coverageData >= 8X There is a 33.01% of reference with a coverageData >= 9X There is a 29.47% of reference with a coverageData >= 10X There is a 26.32% of reference with a coverageData >= 11X There is a 23.5% of reference with a coverageData >= 12X There is a 20.97% of reference with a coverageData >= 13X There is a 18.72% of reference with a coverageData >= 14X There is a 16.71% of reference with a coverageData >= 15X There is a 14.91% of reference with a coverageData >= 16X There is a 13.31% of reference with a coverageData >= 17X There is a 11.88% of reference with a coverageData >= 18X There is a 10.61% of reference with a coverageData >= 19X There is a 9.48% of reference with a coverageData >= 20X There is a 8.47% of reference with a coverageData >= 21X There is a 7.58% of reference with a coverageData >= 22X There is a 6.78% of reference with a coverageData >= 23X There is a 6.08% of reference with a coverageData >= 24X There is a 5.45% of reference with a coverageData >= 25X There is a 4.9% of reference with a coverageData >= 26X There is a 4.41% of reference with a coverageData >= 27X There is a 3.97% of reference with a coverageData >= 28X There is a 3.58% of reference with a coverageData >= 29X There is a 3.24% of reference with a coverageData >= 30X There is a 2.94% of reference with a coverageData >= 31X There is a 2.67% of reference with a coverageData >= 32X There is a 2.43% of reference with a coverageData >= 33X There is a 2.21% of reference with a coverageData >= 34X There is a 2.02% of reference with a coverageData >= 35X There is a 1.85% of reference with a coverageData >= 36X There is a 1.7% of reference with a coverageData >= 37X There is a 1.57% of reference with a coverageData >= 38X There is a 1.45% of reference with a coverageData >= 39X There is a 1.34% of reference with a coverageData >= 40X There is a 1.25% of reference with a coverageData >= 41X There is a 1.16% of reference with a coverageData >= 42X There is a 1.08% of reference with a coverageData >= 43X There is a 1.02% of reference with a coverageData >= 44X There is a 0.95% of reference with a coverageData >= 45X There is a 0.9% of reference with a coverageData >= 46X There is a 0.85% of reference with a coverageData >= 47X There is a 0.8% of reference with a coverageData >= 48X There is a 0.76% of reference with a coverageData >= 49X There is a 0.72% of reference with a coverageData >= 50X There is a 0.68% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2135999103 8.569684177436814 63.16927579632271 chr2 243199373 2194423835 9.023147584348418 233.55304755301924 chr3 198022430 1469328896 7.420012450104768 20.123851036611242 chr4 191154276 2073330017 10.846370064983532 621.8095109498139 chr5 180915260 1432584512 7.918538834148098 33.14622926132208 chr6 171115067 1178657958 6.888101548649717 30.706815617598753 chr7 159138663 1360693163 8.550361912994079 33.24732397971642 chr8 146364022 1294383924 8.84359357110315 155.109832000905 chr9 141213431 1010866659 7.158431403029929 66.52964783069918 chr10 135534747 1816276558 13.40081859598705 471.41556897440574 chr11 135006516 1187602671 8.796632238106197 27.619139928144836 chr12 133851895 1105727107 8.26082519788009 17.070938544198793 chr13 115169878 613282443 5.325024682235054 13.555049864043133 chr14 107349540 737654433 6.871519272462649 29.83171699636033 chr15 102531392 808661290 7.886962950819979 14.44394630186223 chr16 90354753 1250615820 13.841173579435273 180.82804550446852 chr17 81195210 957736761 11.795483514360022 65.70440938176776 chr18 78077248 628825551 8.053889796423153 255.77636621464154 chr19 59128983 937472922 15.85471074312237 37.89869776037533 chr20 63025520 712282722 11.301496949172336 147.75713918032795 chr21 48129895 462297517 9.605205184844056 196.35286040716232 chr22 51304566 518069568 10.097923214085858 29.413069119661113 chrMT 16571 10800086 651.746183090942 286.1036596238675 chrX 155270560 1345842210 8.667723037773548 19.049747950408875 chrY 59373566 443833899 7.475277786077394 526.0968894060151