BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818839.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,290,976 number of mapped reads = 1,992,789 (86.98%) number of supplementary alignments = 33,292 (1.45%) number of secondary alignments = 0 number of mapped bases = 184,550,693 bp number of sequenced bases = 184,437,293 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 533,992 duplication rate = 23.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3581 >>>>>>> ACTG content number of A's = 52,736,286 bp (28.59%) number of C's = 37,186,689 bp (20.16%) number of T's = 55,096,837 bp (29.87%) number of G's = 39,414,664 bp (21.37%) number of N's = 2,817 bp (0%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,109,086 number of insertions = 25,718 mapped reads with insertion percentage = 1.25% number of deletions = 60,436 mapped reads with deletion percentage = 2.96% homopolymer indels = 41.58% >>>>>>> Coverage mean coverageData = 0.0596X std coverageData = 0.662X There is a 3.85% of reference with a coverageData >= 1X There is a 1.22% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 16219747 0.06507404850156823 0.9515126430340748 chr2 243199373 14166307 0.05824976777386675 1.016867398748202 chr3 198022430 12041396 0.0608082427834059 0.35210012709494615 chr4 191154276 9413864 0.04924746752722393 0.3858686173828252 chr5 180915260 8243671 0.04556647681350926 0.3193081062995836 chr6 171115067 9197723 0.05375168394727041 0.37209312608014183 chr7 159138663 16725433 0.10509974562247014 1.356512972793128 chr8 146364022 16444214 0.11235147664909072 0.6155430550702371 chr9 141213431 6874575 0.04868216111822961 0.5997254689025556 chr10 135534747 8408325 0.062038150261202026 0.8533342032498167 chr11 135006516 8141572 0.06030503001795854 0.4273558949955951 chr12 133851895 7244369 0.05412227447358889 0.34135265533990994 chr13 115169878 5781871 0.05020297928942844 0.3168621723622496 chr14 107349540 5492561 0.05116520294358038 0.35795923164961285 chr15 102531392 5107220 0.04981128121229447 0.31282030283495876 chr16 90354753 4473836 0.049514119085688826 0.6662156670312496 chr17 81195210 4400928 0.05420181806291283 0.423000760466183 chr18 78077248 3657102 0.04683953512295925 0.6668682716680282 chr19 59128983 3015964 0.05100652585213583 0.7520784811790322 chr20 63025520 7520529 0.11932514003851138 0.522506334315502 chr21 48129895 1808986 0.03758549649858991 0.3038751753678389 chr22 51304566 1619069 0.03155799037457992 0.293593283445307 chrMT 16571 201697 12.171685474624343 8.740389321021754 chrX 155270560 7756437 0.04995433132977688 0.37467868736426324 chrY 59373566 593297 0.009992611863670106 0.769399647839305