BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524445.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,083,027 number of mapped reads = 2,864,808 (92.92%) number of supplementary alignments = 6,642 (0.22%) number of secondary alignments = 0 number of mapped bases = 167,439,767 bp number of sequenced bases = 167,386,899 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 198,694 duplication rate = 5.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0265 >>>>>>> ACTG content number of A's = 40,225,028 bp (24.03%) number of C's = 33,929,746 bp (20.27%) number of T's = 53,645,642 bp (32.05%) number of G's = 39,583,175 bp (23.65%) number of N's = 3,308 bp (0%) GC percentage = 43.92% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 767,686 number of insertions = 9,067 mapped reads with insertion percentage = 0.32% number of deletions = 30,796 mapped reads with deletion percentage = 1.07% homopolymer indels = 45.2% >>>>>>> Coverage mean coverageData = 0.0541X std coverageData = 0.441X There is a 4.43% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13468146 0.05403455343848471 0.8129518769494469 chr2 243199373 14186973 0.05833474332189171 0.500551670289459 chr3 198022430 11228573 0.056703541108954175 0.2841818106103965 chr4 191154276 10956080 0.057315380169680324 0.3332705415317389 chr5 180915260 10002294 0.055287176991039896 0.2814860362837554 chr6 171115067 9605143 0.05613265487603146 0.3634131265000553 chr7 159138663 9188319 0.0577378169879434 0.6042858029052103 chr8 146364022 8464117 0.05782921844003439 0.4201993671033438 chr9 141213431 7020508 0.0497155826487921 0.384734318993524 chr10 135534747 8034936 0.05928321834695276 0.42527280534615075 chr11 135006516 7663683 0.056765282351260736 0.44445494871335894 chr12 133851895 7582186 0.056646086332957785 0.28934540101498196 chr13 115169878 5341440 0.046378793593929137 0.2589350480286276 chr14 107349540 4975072 0.04634460473701145 0.26490345240818025 chr15 102531392 4721156 0.046045956344765125 0.2732338742986787 chr16 90354753 4932389 0.05458914817685352 0.30804136941676485 chr17 81195210 4462963 0.054965840965249056 0.3100147744018877 chr18 78077248 4471705 0.05727283062025957 0.7247197215291652 chr19 59128983 3269538 0.055295014967532925 0.5871651428985828 chr20 63025520 3587323 0.05691857837904392 0.2935595881616073 chr21 48129895 2265005 0.04706025226109469 0.2875275635913911 chr22 51304566 1994882 0.038883127868190134 0.23339204400472904 chrMT 16571 19581 1.181642628688673 1.3502695499874662 chrX 155270560 9481392 0.061063681357238615 0.3517238715968617 chrY 59373566 516363 0.008696850042660399 0.2137183262466683