BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438259.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 807,735,190 number of mapped reads = 803,648,589 (99.49%) number of supplementary alignments = 21,040,776 (2.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 401,975,684 number of mapped paired reads (second in pair) = 401,672,905 number of mapped paired reads (both in pair) = 801,118,384 number of mapped paired reads (singletons) = 2,530,205 number of mapped bases = 114,000,405,137 bp number of sequenced bases = 113,963,906,729 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 349,474,390 duplication rate = 38.48% >>>>>>> Insert size mean insert size = 99,261.9305 std insert size = 3,014,425.8083 median insert size = 464 >>>>>>> Mapping quality mean mapping quality = 54.2807 >>>>>>> ACTG content number of A's = 35,075,557,392 bp (30.78%) number of C's = 21,576,260,252 bp (18.93%) number of T's = 33,024,738,162 bp (28.98%) number of G's = 24,287,140,229 bp (21.31%) number of N's = 210,694 bp (0%) GC percentage = 40.24% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 624,226,108 number of insertions = 15,097,556 mapped reads with insertion percentage = 1.83% number of deletions = 13,436,895 mapped reads with deletion percentage = 1.63% homopolymer indels = 48.2% >>>>>>> Coverage mean coverageData = 36.8255X std coverageData = 100.7546X There is a 90.76% of reference with a coverageData >= 1X There is a 90% of reference with a coverageData >= 2X There is a 89.21% of reference with a coverageData >= 3X There is a 88.37% of reference with a coverageData >= 4X There is a 87.47% of reference with a coverageData >= 5X There is a 86.51% of reference with a coverageData >= 6X There is a 85.49% of reference with a coverageData >= 7X There is a 84.39% of reference with a coverageData >= 8X There is a 83.23% of reference with a coverageData >= 9X There is a 82.01% of reference with a coverageData >= 10X There is a 80.72% of reference with a coverageData >= 11X There is a 79.38% of reference with a coverageData >= 12X There is a 77.99% of reference with a coverageData >= 13X There is a 76.54% of reference with a coverageData >= 14X There is a 75.06% of reference with a coverageData >= 15X There is a 73.54% of reference with a coverageData >= 16X There is a 71.98% of reference with a coverageData >= 17X There is a 70.4% of reference with a coverageData >= 18X There is a 68.8% of reference with a coverageData >= 19X There is a 67.18% of reference with a coverageData >= 20X There is a 65.55% of reference with a coverageData >= 21X There is a 63.91% of reference with a coverageData >= 22X There is a 62.26% of reference with a coverageData >= 23X There is a 60.62% of reference with a coverageData >= 24X There is a 58.99% of reference with a coverageData >= 25X There is a 57.36% of reference with a coverageData >= 26X There is a 55.75% of reference with a coverageData >= 27X There is a 54.15% of reference with a coverageData >= 28X There is a 52.57% of reference with a coverageData >= 29X There is a 51.01% of reference with a coverageData >= 30X There is a 49.47% of reference with a coverageData >= 31X There is a 47.96% of reference with a coverageData >= 32X There is a 46.47% of reference with a coverageData >= 33X There is a 45.01% of reference with a coverageData >= 34X There is a 43.58% of reference with a coverageData >= 35X There is a 42.18% of reference with a coverageData >= 36X There is a 40.82% of reference with a coverageData >= 37X There is a 39.48% of reference with a coverageData >= 38X There is a 38.18% of reference with a coverageData >= 39X There is a 36.9% of reference with a coverageData >= 40X There is a 35.66% of reference with a coverageData >= 41X There is a 34.46% of reference with a coverageData >= 42X There is a 33.29% of reference with a coverageData >= 43X There is a 32.15% of reference with a coverageData >= 44X There is a 31.04% of reference with a coverageData >= 45X There is a 29.97% of reference with a coverageData >= 46X There is a 28.93% of reference with a coverageData >= 47X There is a 27.92% of reference with a coverageData >= 48X There is a 26.94% of reference with a coverageData >= 49X There is a 25.99% of reference with a coverageData >= 50X There is a 25.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8558471663 34.33681179474373 44.81095995958336 chr2 243199373 9802916682 40.30814948688211 143.89799925371204 chr3 198022430 8086077339 40.834148631546434 30.38516839762011 chr4 191154276 7996882739 41.83470496364936 38.028448383370055 chr5 180915260 7410896383 40.96335700482093 31.1755221461724 chr6 171115067 7020235919 41.02640429086236 39.14356439454749 chr7 159138663 6022328953 37.843279813152634 31.755675911159617 chr8 146364022 5958936516 40.713123584428416 34.283515565997796 chr9 141213431 4865691857 34.45629656147934 56.0398895750793 chr10 135534747 5300301164 39.10658544262454 84.30034568032495 chr11 135006516 5078864356 37.61940168873034 32.58784362561779 chr12 133851895 5190860211 38.78062548909001 32.637199055366594 chr13 115169878 3881024144 33.698256969587135 31.268170861527327 chr14 107349540 3406145341 31.72948240858787 31.51070100825278 chr15 102531392 3121618582 30.445491094083653 30.67139585798964 chr16 90354753 2939390502 32.53166440508116 77.559632284445 chr17 81195210 2481994628 30.56823953038609 42.533514273609654 chr18 78077248 3040227297 38.93870973782273 61.48446809943929 chr19 59128983 1575620301 26.647174043226823 34.234461002625444 chr20 63025520 2253934844 35.7622570031949 35.24262004380532 chr21 48129895 1512529690 31.425991891318276 47.790168509730506 chr22 51304566 1107271631 21.58232136687405 29.903310020796578 chrMT 16571 552777466 33358.12358940317 12474.033396421133 chrX 155270560 6696091608 43.125313697586975 34.444094620804044 chrY 59373566 139315321 2.3464199707998 34.98217164476911