BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777303.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 76,362,272 number of mapped reads = 74,768,497 (97.91%) number of supplementary alignments = 3,249,385 (4.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 37,495,668 number of mapped paired reads (second in pair) = 37,272,829 number of mapped paired reads (both in pair) = 74,261,680 number of mapped paired reads (singletons) = 506,817 number of mapped bases = 7,173,177,854 bp number of sequenced bases = 7,168,742,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,151,007 duplication rate = 12.38% >>>>>>> Insert size mean insert size = 139,057.1314 std insert size = 3,541,603.4402 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 52.4502 >>>>>>> ACTG content number of A's = 2,083,617,584 bp (29.07%) number of C's = 1,503,570,258 bp (20.97%) number of T's = 2,041,638,632 bp (28.48%) number of G's = 1,539,799,910 bp (21.48%) number of N's = 116,346 bp (0%) GC percentage = 42.45% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 56,484,216 number of insertions = 2,014,321 mapped reads with insertion percentage = 2.57% number of deletions = 1,421,154 mapped reads with deletion percentage = 1.79% homopolymer indels = 38.02% >>>>>>> Coverage mean coverageData = 2.3171X std coverageData = 41.3661X There is a 43.04% of reference with a coverageData >= 1X There is a 32.08% of reference with a coverageData >= 2X There is a 23.72% of reference with a coverageData >= 3X There is a 18.4% of reference with a coverageData >= 4X There is a 14.48% of reference with a coverageData >= 5X There is a 11.57% of reference with a coverageData >= 6X There is a 9.35% of reference with a coverageData >= 7X There is a 7.64% of reference with a coverageData >= 8X There is a 6.3% of reference with a coverageData >= 9X There is a 5.23% of reference with a coverageData >= 10X There is a 4.38% of reference with a coverageData >= 11X There is a 3.7% of reference with a coverageData >= 12X There is a 3.15% of reference with a coverageData >= 13X There is a 2.69% of reference with a coverageData >= 14X There is a 2.32% of reference with a coverageData >= 15X There is a 2.01% of reference with a coverageData >= 16X There is a 1.75% of reference with a coverageData >= 17X There is a 1.53% of reference with a coverageData >= 18X There is a 1.35% of reference with a coverageData >= 19X There is a 1.19% of reference with a coverageData >= 20X There is a 1.06% of reference with a coverageData >= 21X There is a 0.95% of reference with a coverageData >= 22X There is a 0.85% of reference with a coverageData >= 23X There is a 0.76% of reference with a coverageData >= 24X There is a 0.69% of reference with a coverageData >= 25X There is a 0.62% of reference with a coverageData >= 26X There is a 0.57% of reference with a coverageData >= 27X There is a 0.52% of reference with a coverageData >= 28X There is a 0.47% of reference with a coverageData >= 29X There is a 0.43% of reference with a coverageData >= 30X There is a 0.4% of reference with a coverageData >= 31X There is a 0.37% of reference with a coverageData >= 32X There is a 0.34% of reference with a coverageData >= 33X There is a 0.32% of reference with a coverageData >= 34X There is a 0.29% of reference with a coverageData >= 35X There is a 0.27% of reference with a coverageData >= 36X There is a 0.25% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 588537246 2.3612267991099607 64.54059974717059 chr2 243199373 625821862 2.573287316822153 46.56054116552087 chr3 198022430 451259809 2.2788317919338734 13.530557483134615 chr4 191154276 471247201 2.465271564210261 37.68318547304713 chr5 180915260 358900100 1.9838022508438482 7.674531091883383 chr6 171115067 394806846 2.3072593952232157 11.203940741211197 chr7 159138663 376099786 2.3633463981031437 25.91717049974166 chr8 146364022 354453727 2.4217271577847184 18.849360236232865 chr9 141213431 295132849 2.089977184960544 29.68118721230001 chr10 135534747 428714523 3.163133679660759 118.80477255232987 chr11 135006516 316638212 2.3453550345673686 11.671989453833612 chr12 133851895 308989445 2.3084428128567027 6.49184939298297 chr13 115169878 208345504 1.8090277390065481 4.990962368648832 chr14 107349540 205795844 1.9170631192271528 8.788737149943904 chr15 102531392 191297653 1.8657471557588918 4.901018770155141 chr16 90354753 281203833 3.112219597346473 52.73680350087309 chr17 81195210 192551981 2.371469708619511 14.232764724194302 chr18 78077248 195522979 2.5042247774921575 35.86110160074865 chr19 59128983 139531011 2.3597735648522824 34.75984617025956 chr20 63025520 153883997 2.441614079503033 11.160607047018386 chr21 48129895 94767130 1.9689868427928214 15.236588157820954 chr22 51304566 87674889 1.708910060753657 9.508787661450134 chrMT 16571 77248191 4661.649327137771 1142.3822561346149 chrX 155270560 193106599 1.2436781254604865 7.1917836022956285 chrY 59373566 181646637 3.059385670047172 71.65873564025149