BamQC report ----------------------------------- >>>>>>> Input bam file = SRR611492.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 1,091,314,268 number of mapped reads = 1,062,262,460 (97.34%) number of supplementary alignments = 10,680,183 (0.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 532,842,915 number of mapped paired reads (second in pair) = 529,419,545 number of mapped paired reads (both in pair) = 1,051,211,404 number of mapped paired reads (singletons) = 11,051,056 number of mapped bases = 91,616,117,021 bp number of sequenced bases = 91,543,248,739 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 413,586,221 duplication rate = 30.88% >>>>>>> Insert size mean insert size = 121,300.9623 std insert size = 3,313,326.2447 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 52.162 >>>>>>> ACTG content number of A's = 26,058,986,826 bp (28.47%) number of C's = 19,120,551,081 bp (20.89%) number of T's = 26,189,234,990 bp (28.61%) number of G's = 20,161,920,252 bp (22.02%) number of N's = 12,555,590 bp (0.01%) GC percentage = 42.91% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 970,883,304 number of insertions = 17,632,152 mapped reads with insertion percentage = 1.61% number of deletions = 43,238,446 mapped reads with deletion percentage = 3.97% homopolymer indels = 47.81% >>>>>>> Coverage mean coverageData = 29.5947X std coverageData = 359.8978X There is a 86.66% of reference with a coverageData >= 1X There is a 83.17% of reference with a coverageData >= 2X There is a 79.88% of reference with a coverageData >= 3X There is a 76.73% of reference with a coverageData >= 4X There is a 73.71% of reference with a coverageData >= 5X There is a 70.81% of reference with a coverageData >= 6X There is a 68.05% of reference with a coverageData >= 7X There is a 65.41% of reference with a coverageData >= 8X There is a 62.89% of reference with a coverageData >= 9X There is a 60.48% of reference with a coverageData >= 10X There is a 58.19% of reference with a coverageData >= 11X There is a 56.01% of reference with a coverageData >= 12X There is a 53.93% of reference with a coverageData >= 13X There is a 51.94% of reference with a coverageData >= 14X There is a 50.05% of reference with a coverageData >= 15X There is a 48.24% of reference with a coverageData >= 16X There is a 46.52% of reference with a coverageData >= 17X There is a 44.87% of reference with a coverageData >= 18X There is a 43.3% of reference with a coverageData >= 19X There is a 41.8% of reference with a coverageData >= 20X There is a 40.36% of reference with a coverageData >= 21X There is a 38.99% of reference with a coverageData >= 22X There is a 37.68% of reference with a coverageData >= 23X There is a 36.42% of reference with a coverageData >= 24X There is a 35.22% of reference with a coverageData >= 25X There is a 34.07% of reference with a coverageData >= 26X There is a 32.96% of reference with a coverageData >= 27X There is a 31.9% of reference with a coverageData >= 28X There is a 30.89% of reference with a coverageData >= 29X There is a 29.91% of reference with a coverageData >= 30X There is a 28.98% of reference with a coverageData >= 31X There is a 28.08% of reference with a coverageData >= 32X There is a 27.22% of reference with a coverageData >= 33X There is a 26.39% of reference with a coverageData >= 34X There is a 25.6% of reference with a coverageData >= 35X There is a 24.83% of reference with a coverageData >= 36X There is a 24.09% of reference with a coverageData >= 37X There is a 23.39% of reference with a coverageData >= 38X There is a 22.7% of reference with a coverageData >= 39X There is a 22.04% of reference with a coverageData >= 40X There is a 21.41% of reference with a coverageData >= 41X There is a 20.8% of reference with a coverageData >= 42X There is a 20.21% of reference with a coverageData >= 43X There is a 19.64% of reference with a coverageData >= 44X There is a 19.1% of reference with a coverageData >= 45X There is a 18.57% of reference with a coverageData >= 46X There is a 18.06% of reference with a coverageData >= 47X There is a 17.56% of reference with a coverageData >= 48X There is a 17.09% of reference with a coverageData >= 49X There is a 16.63% of reference with a coverageData >= 50X There is a 16.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6326445480 25.3818644648432 349.8389926958447 chr2 243199373 9177263073 37.735554001613316 484.3765506960014 chr3 198022430 6768625853 34.18110692308947 62.07592779829365 chr4 191154276 4828554279 25.259985703903375 361.4293409765475 chr5 180915260 5446222121 30.103718840522355 56.431046452289465 chr6 171115067 4077970127 23.83174198798052 129.0625441639674 chr7 159138663 6353691969 39.925508039488804 304.2972332322191 chr8 146364022 3773891631 25.784284822399865 129.48488515258313 chr9 141213431 3701788324 26.214137690628025 411.53869165398424 chr10 135534747 4530041368 33.42346865486826 1118.8871121436887 chr11 135006516 4994616875 36.99537639353644 217.14944401451325 chr12 133851895 3921993179 29.300991061800058 50.97527203116621 chr13 115169878 3285850356 28.530466586063415 45.00717016259027 chr14 107349540 2638692857 24.58038345576516 66.997253932813 chr15 102531392 2171778861 21.181599299851502 33.06903648293268 chr16 90354753 2898819637 32.082646908458706 482.159359174597 chr17 81195210 3129992728 38.548982483079975 243.17585224729268 chr18 78077248 1661064642 21.274631016707964 427.4333291324017 chr19 59128983 1713205766 28.974044184050992 201.61326703645227 chr20 63025520 3272957885 51.930676414887174 174.17992477599975 chr21 48129895 1390962201 28.90017110986841 202.3828061034316 chr22 51304566 1003876359 19.566998364239158 55.27835835237577 chrMT 16571 97222690 5867.038199263774 2199.6426154758465 chrX 155270560 3997571438 25.74584285649514 117.93481168212138 chrY 59373566 453017322 7.629949698490402 526.3874451268657