BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975244.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 45,788,144 number of mapped reads = 45,632,338 (99.66%) number of supplementary alignments = 255,920 (0.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 22,808,171 number of mapped paired reads (second in pair) = 22,824,167 number of mapped paired reads (both in pair) = 45,552,484 number of mapped paired reads (singletons) = 79,854 number of mapped bases = 4,163,501,473 bp number of sequenced bases = 4,162,211,848 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,220,350 duplication rate = 40.74% >>>>>>> Insert size mean insert size = 114,604.1642 std insert size = 3,342,920.2626 median insert size = 181 >>>>>>> Mapping quality mean mapping quality = 55.2854 >>>>>>> ACTG content number of A's = 1,097,784,911 bp (26.38%) number of C's = 927,561,013 bp (22.29%) number of T's = 1,109,578,576 bp (26.66%) number of G's = 1,027,121,461 bp (24.68%) number of N's = 165,887 bp (0%) GC percentage = 46.96% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 26,961,837 number of insertions = 367,803 mapped reads with insertion percentage = 0.79% number of deletions = 866,861 mapped reads with deletion percentage = 1.87% homopolymer indels = 48% >>>>>>> Coverage mean coverageData = 1.3449X std coverageData = 24.383X There is a 12.56% of reference with a coverageData >= 1X There is a 6.92% of reference with a coverageData >= 2X There is a 4.14% of reference with a coverageData >= 3X There is a 2.96% of reference with a coverageData >= 4X There is a 2.21% of reference with a coverageData >= 5X There is a 1.81% of reference with a coverageData >= 6X There is a 1.53% of reference with a coverageData >= 7X There is a 1.35% of reference with a coverageData >= 8X There is a 1.23% of reference with a coverageData >= 9X There is a 1.13% of reference with a coverageData >= 10X There is a 1.06% of reference with a coverageData >= 11X There is a 1% of reference with a coverageData >= 12X There is a 0.96% of reference with a coverageData >= 13X There is a 0.92% of reference with a coverageData >= 14X There is a 0.88% of reference with a coverageData >= 15X There is a 0.85% of reference with a coverageData >= 16X There is a 0.83% of reference with a coverageData >= 17X There is a 0.8% of reference with a coverageData >= 18X There is a 0.78% of reference with a coverageData >= 19X There is a 0.76% of reference with a coverageData >= 20X There is a 0.74% of reference with a coverageData >= 21X There is a 0.73% of reference with a coverageData >= 22X There is a 0.71% of reference with a coverageData >= 23X There is a 0.69% of reference with a coverageData >= 24X There is a 0.68% of reference with a coverageData >= 25X There is a 0.67% of reference with a coverageData >= 26X There is a 0.65% of reference with a coverageData >= 27X There is a 0.64% of reference with a coverageData >= 28X There is a 0.63% of reference with a coverageData >= 29X There is a 0.62% of reference with a coverageData >= 30X There is a 0.61% of reference with a coverageData >= 31X There is a 0.59% of reference with a coverageData >= 32X There is a 0.58% of reference with a coverageData >= 33X There is a 0.57% of reference with a coverageData >= 34X There is a 0.57% of reference with a coverageData >= 35X There is a 0.56% of reference with a coverageData >= 36X There is a 0.55% of reference with a coverageData >= 37X There is a 0.54% of reference with a coverageData >= 38X There is a 0.53% of reference with a coverageData >= 39X There is a 0.52% of reference with a coverageData >= 40X There is a 0.51% of reference with a coverageData >= 41X There is a 0.51% of reference with a coverageData >= 42X There is a 0.5% of reference with a coverageData >= 43X There is a 0.49% of reference with a coverageData >= 44X There is a 0.49% of reference with a coverageData >= 45X There is a 0.48% of reference with a coverageData >= 46X There is a 0.47% of reference with a coverageData >= 47X There is a 0.47% of reference with a coverageData >= 48X There is a 0.46% of reference with a coverageData >= 49X There is a 0.45% of reference with a coverageData >= 50X There is a 0.45% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 436417472 1.750918293599758 30.51924213318374 chr2 243199373 328500273 1.350744736500616 24.06515482369213 chr3 198022430 269288678 1.3598897761228361 22.718433819909578 chr4 191154276 180918756 0.9464541405288783 17.59153892955434 chr5 180915260 214632099 1.1863681316877306 21.98084002875662 chr6 171115067 252489615 1.4755545459944799 25.805616987376943 chr7 159138663 208583997 1.3107059784711148 27.10502949278139 chr8 146364022 147774004 1.0096333920094107 16.68900967494437 chr9 141213431 179320011 1.269850960564792 23.39347618587045 chr10 135534747 183793799 1.3560640578758745 24.039299060047792 chr11 135006516 247805372 1.8355067543554713 29.773678626759985 chr12 133851895 226324329 1.6908563677787303 25.430902351045816 chr13 115169878 84433917 0.7331250016605905 16.58323010504219 chr14 107349540 133188281 1.240697268008787 22.08341212894337 chr15 102531392 143769333 1.402198197016578 23.736978141555433 chr16 90354753 146491574 1.621293502954958 26.865563893966993 chr17 81195210 201773184 2.4850380213315537 39.023823490893065 chr18 78077248 76970847 0.9858294057700394 17.765529768152778 chr19 59128983 160348256 2.711838558089186 37.82110052877035 chr20 63025520 108357657 1.719266370194169 27.59469406560089 chr21 48129895 46003343 0.9558164005967601 24.84387898125393 chr22 51304566 74554643 1.4531775397924622 25.361008507120747 chrMT 16571 285692 17.24048035725062 17.69098813189069 chrX 155270560 100086620 0.6445949573441353 14.467718891736872 chrY 59373566 11389721 0.19183151303393164 5.116176329987784