BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008661.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,649,981 number of mapped reads = 1,441,051 (87.34%) number of supplementary alignments = 12,613 (0.76%) number of secondary alignments = 0 number of mapped bases = 93,677,749 bp number of sequenced bases = 93,630,596 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,443 duplication rate = 5.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.646 >>>>>>> ACTG content number of A's = 25,107,406 bp (26.82%) number of C's = 17,155,567 bp (18.32%) number of T's = 29,705,717 bp (31.73%) number of G's = 21,625,664 bp (23.1%) number of N's = 36,242 bp (0.04%) GC percentage = 41.42% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 768,173 number of insertions = 6,850 mapped reads with insertion percentage = 0.47% number of deletions = 28,093 mapped reads with deletion percentage = 1.93% homopolymer indels = 46.51% >>>>>>> Coverage mean coverageData = 0.0303X std coverageData = 0.289X There is a 2.35% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 13258155 0.053192064063102173 0.5618590158273149 chr2 243199373 5553775 0.02283630476300611 0.278662604267358 chr3 198022430 6488643 0.032767212279942226 0.22382687147250682 chr4 191154276 6863340 0.03590471604203089 0.2433620879440553 chr5 180915260 5058128 0.02795854810699772 0.20611034149897467 chr6 171115067 4706737 0.02750626863267394 0.2141940212257967 chr7 159138663 6662043 0.041863132908185864 0.39739463775016126 chr8 146364022 4347480 0.029703201241627536 0.32261212516459425 chr9 141213431 3646077 0.025819619098412815 0.23777327374987622 chr10 135534747 4836470 0.035684354802388796 0.28765464206209224 chr11 135006516 1501643 0.011122744623674312 0.15330730995217512 chr12 133851895 4294399 0.03208321406282668 0.22303977026555127 chr13 115169878 1146118 0.00995154305885433 0.12328571135182524 chr14 107349540 4165380 0.03880202933333483 0.2480401942876975 chr15 102531392 3193352 0.03114511504925243 0.2185353400785875 chr16 90354753 2961013 0.0327709711076295 0.2297989851726222 chr17 81195210 4229927 0.052095770181516864 0.3006523326902067 chr18 78077248 940644 0.012047607005820696 0.3056885607042794 chr19 59128983 3066949 0.05186879334623428 0.3963805339076099 chr20 63025520 2104271 0.03338760235536335 0.2285270914478209 chr21 48129895 758669 0.01576294733242198 0.16545858777208977 chr22 51304566 1325293 0.025831872352258083 0.1948314029143512 chrMT 16571 67918 4.098605998430994 3.691794994312861 chrX 155270560 2271765 0.014631009252494484 0.15590056418930098 chrY 59373566 229560 0.0038663670630798897 0.15755281673829344