BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617550.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 47,910,156 number of mapped reads = 47,141,930 (98.4%) number of supplementary alignments = 895,802 (1.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 23,741,965 number of mapped paired reads (second in pair) = 23,399,965 number of mapped paired reads (both in pair) = 46,734,376 number of mapped paired reads (singletons) = 407,554 number of mapped bases = 6,299,534,979 bp number of sequenced bases = 6,294,874,168 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,324,248 duplication rate = 25.09% >>>>>>> Insert size mean insert size = 112,320.488 std insert size = 3,239,352.206 median insert size = 273 >>>>>>> Mapping quality mean mapping quality = 53.5426 >>>>>>> ACTG content number of A's = 1,817,378,566 bp (28.87%) number of C's = 1,194,049,119 bp (18.97%) number of T's = 1,878,790,142 bp (29.85%) number of G's = 1,404,399,553 bp (22.31%) number of N's = 256,788 bp (0%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 70,388,099 number of insertions = 1,079,778 mapped reads with insertion percentage = 2.16% number of deletions = 2,488,795 mapped reads with deletion percentage = 5.07% homopolymer indels = 46.25% >>>>>>> Coverage mean coverageData = 2.0349X std coverageData = 21.9193X There is a 38.53% of reference with a coverageData >= 1X There is a 28.67% of reference with a coverageData >= 2X There is a 21.87% of reference with a coverageData >= 3X There is a 17.3% of reference with a coverageData >= 4X There is a 13.84% of reference with a coverageData >= 5X There is a 11.24% of reference with a coverageData >= 6X There is a 9.22% of reference with a coverageData >= 7X There is a 7.62% of reference with a coverageData >= 8X There is a 6.35% of reference with a coverageData >= 9X There is a 5.33% of reference with a coverageData >= 10X There is a 4.49% of reference with a coverageData >= 11X There is a 3.81% of reference with a coverageData >= 12X There is a 3.24% of reference with a coverageData >= 13X There is a 2.77% of reference with a coverageData >= 14X There is a 2.38% of reference with a coverageData >= 15X There is a 2.05% of reference with a coverageData >= 16X There is a 1.77% of reference with a coverageData >= 17X There is a 1.54% of reference with a coverageData >= 18X There is a 1.34% of reference with a coverageData >= 19X There is a 1.17% of reference with a coverageData >= 20X There is a 1.02% of reference with a coverageData >= 21X There is a 0.89% of reference with a coverageData >= 22X There is a 0.79% of reference with a coverageData >= 23X There is a 0.69% of reference with a coverageData >= 24X There is a 0.61% of reference with a coverageData >= 25X There is a 0.54% of reference with a coverageData >= 26X There is a 0.48% of reference with a coverageData >= 27X There is a 0.43% of reference with a coverageData >= 28X There is a 0.38% of reference with a coverageData >= 29X There is a 0.34% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.27% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 581745324 2.3339774306921384 17.26794653909131 chr2 243199373 558293814 2.295621929913446 23.03990425290674 chr3 198022430 323356366 1.6329279768963547 4.0435437708226845 chr4 191154276 389451762 2.0373688214016203 16.256866217158755 chr5 180915260 440605218 2.435423180996451 5.38664408739837 chr6 171115067 355584694 2.0780443255765433 13.003074100392794 chr7 159138663 321684241 2.021408468160877 25.196448920611786 chr8 146364022 307835973 2.1032216031887945 6.998182194565976 chr9 141213431 257711991 1.8249821506001083 33.09447901332159 chr10 135534747 325638865 2.402622738507049 65.603612491326 chr11 135006516 283412599 2.099251261324305 17.913647809459587 chr12 133851895 391734642 2.926627538594056 8.940013533411348 chr13 115169878 155219667 1.3477453453584451 3.5010799593164537 chr14 107349540 178741047 1.6650378473908691 4.2977345193120176 chr15 102531392 173014698 1.6874314746453456 5.197242062144227 chr16 90354753 227323465 2.5158993572811825 39.2528562961809 chr17 81195210 127861405 1.5747407390165011 20.09930721349144 chr18 78077248 175305895 2.2452878334031445 30.122552302753824 chr19 59128983 71649847 1.211755104937286 8.795988545229045 chr20 63025520 134281290 2.130585991198486 6.2739025630876375 chr21 48129895 77979547 1.6201894269663377 8.344053829186485 chr22 51304566 60497010 1.179173993987202 3.7244355424214803 chrMT 16571 1760207 106.22213505521694 56.9007017886122 chrX 155270560 359376082 2.3145152693466167 8.048862072671616 chrY 59373566 19469330 0.3279124248659749 20.40118783584201