BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153380.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 = 41,837,836 number of mapped reads = 41,498,080 (99.19%) number of supplementary alignments = 335,540 (0.8%) number of secondary alignments = 0 number of mapped bases = 4,026,009,148 bp number of sequenced bases = 4,025,281,239 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,086,970 duplication rate = 31.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.7603 >>>>>>> ACTG content number of A's = 1,054,424,832 bp (26.2%) number of C's = 954,183,742 bp (23.7%) number of T's = 1,074,818,829 bp (26.7%) number of G's = 940,162,558 bp (23.36%) number of N's = 1,691,278 bp (0.04%) GC percentage = 47.06% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 11,360,562 number of insertions = 435,242 mapped reads with insertion percentage = 1.04% number of deletions = 342,996 mapped reads with deletion percentage = 0.82% homopolymer indels = 49.85% >>>>>>> Coverage mean coverageData = 1.3005X std coverageData = 13.0341X There is a 18.85% of reference with a coverageData >= 1X There is a 9.6% of reference with a coverageData >= 2X There is a 5.3% of reference with a coverageData >= 3X There is a 3.91% of reference with a coverageData >= 4X There is a 3.11% of reference with a coverageData >= 5X There is a 2.69% of reference with a coverageData >= 6X There is a 2.41% of reference with a coverageData >= 7X There is a 2.21% of reference with a coverageData >= 8X There is a 2.05% of reference with a coverageData >= 9X There is a 1.92% of reference with a coverageData >= 10X There is a 1.81% of reference with a coverageData >= 11X There is a 1.71% of reference with a coverageData >= 12X There is a 1.63% of reference with a coverageData >= 13X There is a 1.55% of reference with a coverageData >= 14X There is a 1.48% of reference with a coverageData >= 15X There is a 1.42% of reference with a coverageData >= 16X There is a 1.36% of reference with a coverageData >= 17X There is a 1.3% of reference with a coverageData >= 18X There is a 1.25% of reference with a coverageData >= 19X There is a 1.21% of reference with a coverageData >= 20X There is a 1.16% of reference with a coverageData >= 21X There is a 1.12% of reference with a coverageData >= 22X There is a 1.08% of reference with a coverageData >= 23X There is a 1.05% of reference with a coverageData >= 24X There is a 1.01% of reference with a coverageData >= 25X There is a 0.98% of reference with a coverageData >= 26X There is a 0.95% of reference with a coverageData >= 27X There is a 0.92% of reference with a coverageData >= 28X There is a 0.9% of reference with a coverageData >= 29X There is a 0.87% of reference with a coverageData >= 30X There is a 0.85% of reference with a coverageData >= 31X There is a 0.82% of reference with a coverageData >= 32X There is a 0.8% of reference with a coverageData >= 33X There is a 0.78% of reference with a coverageData >= 34X There is a 0.76% of reference with a coverageData >= 35X There is a 0.74% of reference with a coverageData >= 36X There is a 0.72% of reference with a coverageData >= 37X There is a 0.7% of reference with a coverageData >= 38X There is a 0.68% of reference with a coverageData >= 39X There is a 0.67% of reference with a coverageData >= 40X There is a 0.65% of reference with a coverageData >= 41X There is a 0.64% of reference with a coverageData >= 42X There is a 0.62% of reference with a coverageData >= 43X There is a 0.61% of reference with a coverageData >= 44X There is a 0.59% of reference with a coverageData >= 45X There is a 0.58% of reference with a coverageData >= 46X There is a 0.57% of reference with a coverageData >= 47X There is a 0.55% of reference with a coverageData >= 48X There is a 0.54% of reference with a coverageData >= 49X There is a 0.53% of reference with a coverageData >= 50X There is a 0.52% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 362813507 1.4556172640388325 15.60703929678875 chr2 243199373 355141294 1.460288690793623 11.54355487071785 chr3 198022430 102562819 0.5179353621708409 5.0625617342254206 chr4 191154276 70478453 0.368699327447951 4.386440038336388 chr5 180915260 198047955 1.0947001098746452 9.865163528829225 chr6 171115067 52256148 0.305386012559607 5.400871738380187 chr7 159138663 165573394 1.0404347433784837 8.892335884606789 chr8 146364022 222022318 1.5169186728142794 13.84920338006956 chr9 141213431 77538948 0.5490904615156613 4.955798345967354 chr10 135534747 168473179 1.2430257386321752 9.977357106286934 chr11 135006516 191189212 1.4161480324401527 11.001576591573432 chr12 133851895 262494012 1.9610780407703603 14.337421171479424 chr13 115169878 58605764 0.5088636457529285 5.435655202123365 chr14 107349540 91826062 0.8553931577163721 7.35057011820918 chr15 102531392 239566881 2.336522272125204 19.44172107873898 chr16 90354753 249358422 2.75977094420257 21.346365714464575 chr17 81195210 213039547 2.623794519405763 17.416819603844075 chr18 78077248 11290480 0.14460653121380507 2.3308248527331297 chr19 59128983 307907293 5.207383543194037 37.3746742087541 chr20 63025520 137951484 2.1888194496451594 17.064433135875873 chr21 48129895 56054717 1.1646548782206985 11.373064715745503 chr22 51304566 62735160 1.2227987660981285 10.230485086921618 chrMT 16571 14963 0.9029630076639913 1.9286025630013954 chrX 155270560 365142161 2.3516509568845505 21.28873834718992 chrY 59373566 3924975 0.06610643868013587 2.5459717303741156