BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365366.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 548,656,868 number of mapped reads = 461,117,606 (84.04%) number of supplementary alignments = 17,902,456 (3.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 229,163,420 number of mapped paired reads (second in pair) = 231,954,186 number of mapped paired reads (both in pair) = 445,530,460 number of mapped paired reads (singletons) = 15,587,146 number of mapped bases = 56,802,805,339 bp number of sequenced bases = 56,769,729,409 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 326,923,724 duplication rate = 45.96% >>>>>>> Insert size mean insert size = 131,670.0736 std insert size = 3,548,907.6562 median insert size = 147 >>>>>>> Mapping quality mean mapping quality = 52.9788 >>>>>>> ACTG content number of A's = 15,867,823,998 bp (27.95%) number of C's = 11,913,352,330 bp (20.99%) number of T's = 16,103,443,736 bp (28.37%) number of G's = 12,883,526,812 bp (22.69%) number of N's = 1,582,533 bp (0%) GC percentage = 43.68% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 601,527,652 number of insertions = 5,779,982 mapped reads with insertion percentage = 1.19% number of deletions = 15,700,557 mapped reads with deletion percentage = 3.3% homopolymer indels = 42.77% >>>>>>> Coverage mean coverageData = 18.349X std coverageData = 182.2477X There is a 41.44% of reference with a coverageData >= 1X There is a 33.23% of reference with a coverageData >= 2X There is a 26.65% of reference with a coverageData >= 3X There is a 24.36% of reference with a coverageData >= 4X There is a 22.62% of reference with a coverageData >= 5X There is a 21.71% of reference with a coverageData >= 6X There is a 20.88% of reference with a coverageData >= 7X There is a 20.34% of reference with a coverageData >= 8X There is a 19.8% of reference with a coverageData >= 9X There is a 19.39% of reference with a coverageData >= 10X There is a 18.96% of reference with a coverageData >= 11X There is a 18.62% of reference with a coverageData >= 12X There is a 18.25% of reference with a coverageData >= 13X There is a 17.95% of reference with a coverageData >= 14X There is a 17.63% of reference with a coverageData >= 15X There is a 17.35% of reference with a coverageData >= 16X There is a 17.06% of reference with a coverageData >= 17X There is a 16.8% of reference with a coverageData >= 18X There is a 16.53% of reference with a coverageData >= 19X There is a 16.29% of reference with a coverageData >= 20X There is a 16.04% of reference with a coverageData >= 21X There is a 15.81% of reference with a coverageData >= 22X There is a 15.57% of reference with a coverageData >= 23X There is a 15.35% of reference with a coverageData >= 24X There is a 15.13% of reference with a coverageData >= 25X There is a 14.92% of reference with a coverageData >= 26X There is a 14.71% of reference with a coverageData >= 27X There is a 14.51% of reference with a coverageData >= 28X There is a 14.31% of reference with a coverageData >= 29X There is a 14.12% of reference with a coverageData >= 30X There is a 13.92% of reference with a coverageData >= 31X There is a 13.74% of reference with a coverageData >= 32X There is a 13.55% of reference with a coverageData >= 33X There is a 13.38% of reference with a coverageData >= 34X There is a 13.2% of reference with a coverageData >= 35X There is a 13.03% of reference with a coverageData >= 36X There is a 12.85% of reference with a coverageData >= 37X There is a 12.69% of reference with a coverageData >= 38X There is a 12.52% of reference with a coverageData >= 39X There is a 12.36% of reference with a coverageData >= 40X There is a 12.2% of reference with a coverageData >= 41X There is a 12.04% of reference with a coverageData >= 42X There is a 11.88% of reference with a coverageData >= 43X There is a 11.73% of reference with a coverageData >= 44X There is a 11.58% of reference with a coverageData >= 45X There is a 11.43% of reference with a coverageData >= 46X There is a 11.28% of reference with a coverageData >= 47X There is a 11.14% of reference with a coverageData >= 48X There is a 11% of reference with a coverageData >= 49X There is a 10.86% of reference with a coverageData >= 50X There is a 10.72% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4514081453 18.11061266322783 364.01738756651514 chr2 243199373 5220758292 21.46698911102867 227.88938514866905 chr3 198022430 3633969200 18.351300910709963 57.07908123434247 chr4 191154276 3863118747 20.209428885598143 116.84901712082457 chr5 180915260 3434014011 18.981339722254496 73.2257458213221 chr6 171115067 3245199402 18.965012601724897 98.42462640779779 chr7 159138663 3434055267 21.57901293289111 220.26666869545704 chr8 146364022 2679791042 18.309083102403402 99.53231044463669 chr9 141213431 2627478049 18.6064316290141 236.50686347485367 chr10 135534747 2672830057 19.720626010391268 242.8807966779112 chr11 135006516 2568018105 19.021438231914672 230.07343381889902 chr12 133851895 2397976282 17.91514630405494 58.50616282697431 chr13 115169878 1632696625 14.176420548088103 50.32615473991468 chr14 107349540 1756345639 16.360998277216652 154.20949519283846 chr15 102531392 1762507936 17.189934727502774 57.57221370713051 chr16 90354753 1721213271 19.049504468237547 78.38066853579852 chr17 81195210 1743199745 21.469243629026884 150.14330791253536 chr18 78077248 1568609811 20.09048539979278 262.0032795712091 chr19 59128983 1315462712 22.247342086029114 203.74045878799146 chr20 63025520 1317795336 20.908916515087856 80.3161827743732 chr21 48129895 753466845 15.654861599012422 93.327134601035 chr22 51304566 813048428 15.847486712975995 78.14330153925647 chrMT 16571 147304820 8889.313861565386 5734.737959021649 chrX 155270560 1464250167 9.430314201223979 72.27344438710668 chrY 59373566 515614097 8.68423663486879 153.53896671747898