BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618585.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 63,657,516 number of mapped reads = 54,407,376 (85.47%) number of supplementary alignments = 157,454 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,483,657 number of mapped paired reads (second in pair) = 26,923,719 number of mapped paired reads (both in pair) = 53,316,754 number of mapped paired reads (singletons) = 1,090,622 number of mapped bases = 5,128,585,599 bp number of sequenced bases = 5,125,111,441 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,920,537 duplication rate = 15.71% >>>>>>> Insert size mean insert size = 57,205.9967 std insert size = 2,371,643.5085 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 53.5788 >>>>>>> ACTG content number of A's = 1,394,633,398 bp (27.21%) number of C's = 1,123,013,256 bp (21.91%) number of T's = 1,414,109,926 bp (27.59%) number of G's = 1,193,106,004 bp (23.28%) number of N's = 248,857 bp (0%) GC percentage = 45.19% >>>>>>> Mismatches and indels general error rate = 0.0128 number of mismatches = 64,139,138 number of insertions = 910,656 mapped reads with insertion percentage = 1.65% number of deletions = 2,563,005 mapped reads with deletion percentage = 4.59% homopolymer indels = 52.81% >>>>>>> Coverage mean coverageData = 1.6567X std coverageData = 6.1583X There is a 30.72% of reference with a coverageData >= 1X There is a 20.95% of reference with a coverageData >= 2X There is a 15.47% of reference with a coverageData >= 3X There is a 12.16% of reference with a coverageData >= 4X There is a 9.85% of reference with a coverageData >= 5X There is a 8.18% of reference with a coverageData >= 6X There is a 6.9% of reference with a coverageData >= 7X There is a 5.9% of reference with a coverageData >= 8X There is a 5.1% of reference with a coverageData >= 9X There is a 4.45% of reference with a coverageData >= 10X There is a 3.91% of reference with a coverageData >= 11X There is a 3.46% of reference with a coverageData >= 12X There is a 3.07% of reference with a coverageData >= 13X There is a 2.74% of reference with a coverageData >= 14X There is a 2.46% of reference with a coverageData >= 15X There is a 2.21% of reference with a coverageData >= 16X There is a 2% of reference with a coverageData >= 17X There is a 1.81% of reference with a coverageData >= 18X There is a 1.65% of reference with a coverageData >= 19X There is a 1.5% of reference with a coverageData >= 20X There is a 1.37% of reference with a coverageData >= 21X There is a 1.25% of reference with a coverageData >= 22X There is a 1.15% of reference with a coverageData >= 23X There is a 1.05% of reference with a coverageData >= 24X There is a 0.97% of reference with a coverageData >= 25X There is a 0.89% of reference with a coverageData >= 26X There is a 0.83% of reference with a coverageData >= 27X There is a 0.76% of reference with a coverageData >= 28X There is a 0.71% of reference with a coverageData >= 29X There is a 0.66% of reference with a coverageData >= 30X There is a 0.61% of reference with a coverageData >= 31X There is a 0.57% of reference with a coverageData >= 32X There is a 0.53% of reference with a coverageData >= 33X There is a 0.49% of reference with a coverageData >= 34X There is a 0.46% of reference with a coverageData >= 35X There is a 0.43% of reference with a coverageData >= 36X There is a 0.4% of reference with a coverageData >= 37X There is a 0.37% of reference with a coverageData >= 38X There is a 0.35% of reference with a coverageData >= 39X There is a 0.33% of reference with a coverageData >= 40X There is a 0.31% of reference with a coverageData >= 41X There is a 0.29% of reference with a coverageData >= 42X There is a 0.27% of reference with a coverageData >= 43X There is a 0.26% of reference with a coverageData >= 44X There is a 0.24% of reference with a coverageData >= 45X There is a 0.23% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 451410766 1.8110717806396157 7.365944877104377 chr2 243199373 434218781 1.785443669708803 6.969067705803247 chr3 198022430 324184982 1.6371124321623565 5.05537431835509 chr4 191154276 259468587 1.3573778857031689 4.79851382713138 chr5 180915260 290725021 1.606967930731769 5.0091598712893335 chr6 171115067 279406845 1.6328593963031905 5.319308278453299 chr7 159138663 255313519 1.6043462612225163 5.083643959096452 chr8 146364022 247628093 1.6918645006899304 5.2949887023324935 chr9 141213431 228607309 1.6188779451155748 7.494709439615761 chr10 135534747 257873814 1.9026398743342179 5.867418544581799 chr11 135006516 264988469 1.9627828111644625 7.490830845294846 chr12 133851895 230026836 1.7185175899078604 5.374034902013473 chr13 115169878 135755583 1.178742092615571 4.061891350327209 chr14 107349540 152815920 1.4235358623800345 4.821214893491023 chr15 102531392 164208771 1.6015462952068378 5.339667476389046 chr16 90354753 177325523 1.9625478141697759 10.935958423249229 chr17 81195210 167986181 2.0689173782542096 6.828790735558493 chr18 78077248 126919668 1.6255653375487824 7.122725642294105 chr19 59128983 107720482 1.8217881745065698 6.6242399339110225 chr20 63025520 141258375 2.2412885288372077 6.465296093242456 chr21 48129895 67964642 1.4121086696740144 7.198855300629563 chr22 51304566 89580065 1.7460446892777535 6.228085741149903 chrMT 16571 6051 0.3651559954136745 1.2178465817844768 chrX 155270560 266235617 1.7146561266990987 5.250779913544219 chrY 59373566 6955699 0.11715144412919379 3.736008033113967