BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472443.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,208,834 number of mapped reads = 19,046,979 (99.16%) number of supplementary alignments = 64,347 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,547,749 number of mapped paired reads (second in pair) = 9,499,230 number of mapped paired reads (both in pair) = 18,962,224 number of mapped paired reads (singletons) = 84,755 number of mapped bases = 1,860,837,409 bp number of sequenced bases = 1,860,641,762 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,778,087 duplication rate = 48.47% >>>>>>> Insert size mean insert size = 19,263.9061 std insert size = 1,434,132.4079 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 53.8433 >>>>>>> ACTG content number of A's = 491,655,369 bp (26.42%) number of C's = 440,158,690 bp (23.66%) number of T's = 492,348,957 bp (26.46%) number of G's = 436,240,505 bp (23.45%) number of N's = 238,241 bp (0.01%) GC percentage = 47.1% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 9,694,311 number of insertions = 105,265 mapped reads with insertion percentage = 0.55% number of deletions = 84,622 mapped reads with deletion percentage = 0.44% homopolymer indels = 45.88% >>>>>>> Coverage mean coverageData = 0.6011X std coverageData = 21.2918X There is a 4.78% of reference with a coverageData >= 1X There is a 2.24% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 367738660 1.4753771064827157 39.25557846934003 chr2 243199373 175326560 0.7209169901930627 21.21512044488811 chr3 198022430 145021706 0.7323498959183563 19.7838991914576 chr4 191154276 66712611 0.3489987898570472 16.899019023747982 chr5 180915260 18162703 0.10039342728744938 4.717432286927733 chr6 171115067 198390729 1.1593995343495964 31.050540977458205 chr7 159138663 67836667 0.4262739533007136 16.616631158883962 chr8 146364022 62190732 0.424904502829254 14.376573986204136 chr9 141213431 78346663 0.5548102786341903 14.804774891403222 chr10 135534747 30578975 0.22561723599926742 8.290830151330097 chr11 135006516 47515909 0.35195270871222245 10.90724740363843 chr12 133851895 123566600 0.9231591379412297 26.004048849545253 chr13 115169878 83018044 0.7208312229001406 22.924222360167143 chr14 107349540 56586549 0.5271242801785644 20.729146350724836 chr15 102531392 16269960 0.15868271836200176 5.4894569024984 chr16 90354753 68845863 0.7619506524465847 29.97455729608147 chr17 81195210 84735813 1.043606057549454 26.29194524567085 chr18 78077248 8175586 0.10471150315134058 3.725330333813485 chr19 59128983 49396096 0.8353956637475061 29.71229080576383 chr20 63025520 24982901 0.39639341333478884 16.86295747004758 chr21 48129895 4703924 0.09773393438734906 6.763132600741626 chr22 51304566 2091212 0.04076073852763904 2.8883095125230964 chrMT 16571 20377 1.229678353750528 1.5322482640134216 chrX 155270560 80319390 0.5172866640012118 20.67126018183378 chrY 59373566 303179 0.005106295956688874 0.34708424166987367