BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240241.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 = 2,422,137 number of mapped reads = 1,727,250 (71.31%) number of supplementary alignments = 12,553 (0.52%) number of secondary alignments = 0 number of mapped bases = 109,098,989 bp number of sequenced bases = 109,049,018 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 310,755 duplication rate = 13.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5306 >>>>>>> ACTG content number of A's = 29,020,673 bp (26.61%) number of C's = 20,004,195 bp (18.34%) number of T's = 34,762,102 bp (31.88%) number of G's = 25,253,524 bp (23.16%) number of N's = 8,524 bp (0.01%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 959,217 number of insertions = 7,409 mapped reads with insertion percentage = 0.43% number of deletions = 28,916 mapped reads with deletion percentage = 1.66% homopolymer indels = 47.53% >>>>>>> Coverage mean coverageData = 0.0352X std coverageData = 0.3899X There is a 1.75% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% 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 8662444 0.034753951525761696 0.4876952572781439 chr2 243199373 11635589 0.047843828117106205 0.5305169399994564 chr3 198022430 6788850 0.03428323751001339 0.3276669999004172 chr4 191154276 6815289 0.035653343166647235 0.3392184824988922 chr5 180915260 5635129 0.031147892112583536 0.3086245640023069 chr6 171115067 5657838 0.033064522599871346 0.3560350716625992 chr7 159138663 6459268 0.04058892966821017 0.5096683708185533 chr8 146364022 5963289 0.040742860974399844 0.41941069464188374 chr9 141213431 4030019 0.02853849645505745 0.33380946872523665 chr10 135534747 5131748 0.03786296956012321 0.3782075976826744 chr11 135006516 4736209 0.03508133637046081 0.38882949327262356 chr12 133851895 5480028 0.04094098182173663 0.3625223884076438 chr13 115169878 2779921 0.024137570068451405 0.27841275543146726 chr14 107349540 3648570 0.03398775625866678 0.34809442129441337 chr15 102531392 3157092 0.03079146726107064 0.3405081868764368 chr16 90354753 3390007 0.03751885636829753 0.3412361659630232 chr17 81195210 2892752 0.035627126279986224 0.34791577803832713 chr18 78077248 2586573 0.03312838331596933 0.4713231268763971 chr19 59128983 2174654 0.036778139749164974 0.4182281818057606 chr20 63025520 2336554 0.03707314116567384 0.3485806969545967 chr21 48129895 1735441 0.036057444131137206 0.33493910692260404 chr22 51304566 1096399 0.021370398104527382 0.25604747098807956 chrMT 16571 20094 1.2126003258704967 1.8162436035693246 chrX 155270560 5981393 0.03852238956309554 0.3684328095434392 chrY 59373566 303839 0.0051174120146329095 0.11962195605992033