BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038437.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 77,424,954 number of mapped reads = 76,899,528 (99.32%) number of supplementary alignments = 171,875 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 38,608,793 number of mapped paired reads (second in pair) = 38,290,735 number of mapped paired reads (both in pair) = 76,533,412 number of mapped paired reads (singletons) = 366,116 number of mapped bases = 11,416,731,250 bp number of sequenced bases = 11,414,751,077 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,104,399 duplication rate = 36.32% >>>>>>> Insert size mean insert size = 23,156.7728 std insert size = 1,601,124.7261 median insert size = 228 >>>>>>> Mapping quality mean mapping quality = 55.8073 >>>>>>> ACTG content number of A's = 2,811,067,667 bp (24.63%) number of C's = 2,896,945,565 bp (25.38%) number of T's = 2,830,387,286 bp (24.8%) number of G's = 2,875,291,589 bp (25.19%) number of N's = 1,058,970 bp (0.01%) GC percentage = 50.57% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 69,884,392 number of insertions = 598,933 mapped reads with insertion percentage = 0.74% number of deletions = 705,031 mapped reads with deletion percentage = 0.89% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 3.6879X std coverageData = 24.4307X There is a 22.74% of reference with a coverageData >= 1X There is a 14.56% of reference with a coverageData >= 2X There is a 9.32% of reference with a coverageData >= 3X There is a 7.23% of reference with a coverageData >= 4X There is a 5.76% of reference with a coverageData >= 5X There is a 4.97% of reference with a coverageData >= 6X There is a 4.44% of reference with a coverageData >= 7X There is a 4.1% of reference with a coverageData >= 8X There is a 3.86% of reference with a coverageData >= 9X There is a 3.69% of reference with a coverageData >= 10X There is a 3.55% of reference with a coverageData >= 11X There is a 3.45% of reference with a coverageData >= 12X There is a 3.36% of reference with a coverageData >= 13X There is a 3.28% of reference with a coverageData >= 14X There is a 3.21% of reference with a coverageData >= 15X There is a 3.15% of reference with a coverageData >= 16X There is a 3.09% of reference with a coverageData >= 17X There is a 3.04% of reference with a coverageData >= 18X There is a 2.99% of reference with a coverageData >= 19X There is a 2.94% of reference with a coverageData >= 20X There is a 2.89% of reference with a coverageData >= 21X There is a 2.85% of reference with a coverageData >= 22X There is a 2.81% of reference with a coverageData >= 23X There is a 2.77% of reference with a coverageData >= 24X There is a 2.73% of reference with a coverageData >= 25X There is a 2.69% of reference with a coverageData >= 26X There is a 2.66% of reference with a coverageData >= 27X There is a 2.62% of reference with a coverageData >= 28X There is a 2.59% of reference with a coverageData >= 29X There is a 2.56% of reference with a coverageData >= 30X There is a 2.52% of reference with a coverageData >= 31X There is a 2.49% of reference with a coverageData >= 32X There is a 2.46% of reference with a coverageData >= 33X There is a 2.43% of reference with a coverageData >= 34X There is a 2.4% of reference with a coverageData >= 35X There is a 2.38% of reference with a coverageData >= 36X There is a 2.35% of reference with a coverageData >= 37X There is a 2.32% of reference with a coverageData >= 38X There is a 2.29% of reference with a coverageData >= 39X There is a 2.27% of reference with a coverageData >= 40X There is a 2.24% of reference with a coverageData >= 41X There is a 2.22% of reference with a coverageData >= 42X There is a 2.19% of reference with a coverageData >= 43X There is a 2.17% of reference with a coverageData >= 44X There is a 2.14% of reference with a coverageData >= 45X There is a 2.12% of reference with a coverageData >= 46X There is a 2.09% of reference with a coverageData >= 47X There is a 2.07% of reference with a coverageData >= 48X There is a 2.05% of reference with a coverageData >= 49X There is a 2.03% of reference with a coverageData >= 50X There is a 2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 991474498 3.9778215758186617 23.913725471219525 chr2 243199373 948002780 3.8980477963650015 25.96421161611714 chr3 198022430 644569625 3.255033407074138 21.428337584468995 chr4 191154276 356642348 1.8657304218504638 14.187908063482963 chr5 180915260 493448174 2.7275099623989707 20.720790905769427 chr6 171115067 661442228 3.8654820969096777 25.92936720039059 chr7 159138663 754931554 4.743860101426138 32.761789380943846 chr8 146364022 344878928 2.356309448779701 16.958553615726544 chr9 141213431 450668937 3.1914027851925786 21.39868204777409 chr10 135534747 354400665 2.61483252704194 16.397420927198166 chr11 135006516 770547295 5.707482259597011 33.98175205382532 chr12 133851895 484804838 3.6219497527472435 20.368619023847835 chr13 115169878 351220077 3.049582782400794 25.454367509975505 chr14 107349540 272322049 2.536778909346048 16.419255576260987 chr15 102531392 299515702 2.9212097500831744 17.382382603067537 chr16 90354753 579753208 6.416410744878025 34.0383756062195 chr17 81195210 696300230 8.575631863012608 37.41020469108772 chr18 78077248 110011918 1.4090137756904546 10.613439788179608 chr19 59128983 754510839 12.760423073740334 45.38415907007608 chr20 63025520 443485123 7.036596016978519 40.25029735938765 chr21 48129895 94070148 1.9545055728877032 25.3593985118542 chr22 51304566 195375891 3.808157952257115 20.302397905068553 chrMT 16571 1213218 73.21332448252971 27.883741331052263 chrX 155270560 342857758 2.2081311357413793 16.521241662683952 chrY 59373566 20283219 0.34162036014478225 4.9625535830764775