BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549072.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,492,901 number of mapped reads = 8,993,696 (85.71%) number of secondary alignments = 0 number of mapped bases = 356,642,592 bp number of sequenced bases = 356,609,738 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 422,585 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.4458 >>>>>>> ACTG content number of A's = 105,087,027 bp (29.47%) number of C's = 72,892,565 bp (20.44%) number of T's = 105,576,730 bp (29.61%) number of G's = 73,046,979 bp (20.48%) number of N's = 6,437 bp (0%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 1,209,620 number of insertions = 9,985 mapped reads with insertion percentage = 0.11% number of deletions = 26,472 mapped reads with deletion percentage = 0.29% homopolymer indels = 42.7% >>>>>>> Coverage mean coverageData = 0.1152X std coverageData = 1.3621X There is a 9.46% of reference with a coverageData >= 1X There is a 1.41% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% 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 28485365 0.1142840282030832 3.623480046702666 chr2 243199373 31355275 0.12892827236030743 0.9163049380163875 chr3 198022430 25107570 0.1267915457860001 0.4318108622325408 chr4 191154276 25548288 0.1336527151503532 0.49506840399689234 chr5 180915260 23236887 0.1284407241268647 0.4512966411979171 chr6 171115067 21304252 0.12450249047911134 0.5696071268514901 chr7 159138663 20488729 0.12874765072017727 1.302680355559319 chr8 146364022 19193882 0.13113797870353686 1.5090242631751272 chr9 141213431 15106953 0.10697957618493102 0.8898589176234674 chr10 135534747 17485933 0.12901439215436025 1.3291735204835158 chr11 135006516 16490745 0.12214777100091968 0.7893856397547913 chr12 133851895 16507702 0.12332811575062123 0.4908358579559031 chr13 115169878 11855365 0.10293807031730988 0.36080020027672155 chr14 107349540 10992201 0.10239634934625709 0.5130870913394859 chr15 102531392 9482330 0.0924822126671215 0.3486300134745679 chr16 90354753 9293773 0.1028587062818931 0.6318777814589365 chr17 81195210 8259342 0.10172203508064084 0.47141579031073194 chr18 78077248 9859379 0.12627723507877736 1.9782661492240758 chr19 59128983 6220214 0.10519737841592845 2.942583467852216 chr20 63025520 6729173 0.10676901991447274 0.42856657534620257 chr21 48129895 4550928 0.09455512005584056 0.511491216552905 chr22 51304566 3280452 0.06394074164860881 0.3629931836436573 chrMT 16571 31144 1.8794279162392131 2.2683903368674243 chrX 155270560 12660110 0.08153580434050087 0.5483943669562955 chrY 59373566 3116600 0.05249137301269727 0.47042701459611425