BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068093.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 = 1,829,669 number of mapped reads = 1,497,447 (81.84%) number of supplementary alignments = 15,842 (0.87%) number of secondary alignments = 0 number of mapped bases = 94,058,304 bp number of sequenced bases = 94,022,388 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 165,973 duplication rate = 8.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0289 >>>>>>> ACTG content number of A's = 25,388,268 bp (27%) number of C's = 17,072,122 bp (18.16%) number of T's = 30,100,946 bp (32.01%) number of G's = 21,459,261 bp (22.82%) number of N's = 1,791 bp (0%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 732,221 number of insertions = 7,043 mapped reads with insertion percentage = 0.47% number of deletions = 22,529 mapped reads with deletion percentage = 1.49% homopolymer indels = 46.34% >>>>>>> Coverage mean coverageData = 0.0304X std coverageData = 0.3303X There is a 1.97% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 8312300 0.03334916465463891 0.45883183537309724 chr2 243199373 10111594 0.04157738515222241 0.5330143405597157 chr3 198022430 5291398 0.026721205269524265 0.2387324147070462 chr4 191154276 4987295 0.026090418191848347 0.24786635259320655 chr5 180915260 4932163 0.02726228290526736 0.24061785491612717 chr6 171115067 6413291 0.03747940559787175 0.32633703219769833 chr7 159138663 5119459 0.03216980024521131 0.37986506381600466 chr8 146364022 4343450 0.029675667152683192 0.34293547142872705 chr9 141213431 4506354 0.031911652936185655 0.3068415811132011 chr10 135534747 4241226 0.0312925363707655 0.3148279642098197 chr11 135006516 3441139 0.025488688264498287 0.25985410122836694 chr12 133851895 4106932 0.030682658620559685 0.2592070481264217 chr13 115169878 3079596 0.026739595921079294 0.24477264296065804 chr14 107349540 2873388 0.02676665405366432 0.26239732154615686 chr15 102531392 3510741 0.03424064505044465 0.28991755269295416 chr16 90354753 2470576 0.02734306628008822 0.2527533243116224 chr17 81195210 2120929 0.02612135617359694 0.2385627816763926 chr18 78077248 2386526 0.03056621565350254 0.4416679425005086 chr19 59128983 1764474 0.02984110178252178 0.3540748920696688 chr20 63025520 1980374 0.03142177962196901 0.2634439334578418 chr21 48129895 1210817 0.025157274911985574 0.24046896085182423 chr22 51304566 906665 0.017672208746488567 0.18878184325611932 chrMT 16571 71175 4.295154185022026 3.7938138855260504 chrX 155270560 5607298 0.03611307900222682 0.2906837063223829 chrY 59373566 269144 0.004533061059529421 0.1163486051573679