BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524423.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 = 2,348,254 number of mapped reads = 2,177,703 (92.74%) number of supplementary alignments = 9,776 (0.42%) number of secondary alignments = 0 number of mapped bases = 128,470,113 bp number of sequenced bases = 128,431,575 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,129 duplication rate = 4.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7345 >>>>>>> ACTG content number of A's = 32,299,218 bp (25.15%) number of C's = 26,124,039 bp (20.34%) number of T's = 39,274,929 bp (30.58%) number of G's = 30,720,457 bp (23.92%) number of N's = 12,932 bp (0.01%) GC percentage = 44.26% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 649,902 number of insertions = 8,998 mapped reads with insertion percentage = 0.41% number of deletions = 23,788 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.87% >>>>>>> Coverage mean coverageData = 0.0415X std coverageData = 0.4019X There is a 3.54% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% 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 10821803 0.04341735621994699 0.8631290697274535 chr2 243199373 10384159 0.04269813228506967 0.48883427038362265 chr3 198022430 8634343 0.04360285347473011 0.23985279508303173 chr4 191154276 8426043 0.044079803896199525 0.3252807816599823 chr5 180915260 7763820 0.04291412454648657 0.2354086931988569 chr6 171115067 4870305 0.0284621634166207 0.2075978882492711 chr7 159138663 7269895 0.04568277037742865 0.5314548172140036 chr8 146364022 6673976 0.045598473646754525 0.3108558250968162 chr9 141213431 4777970 0.03383509603983774 0.2698283899140872 chr10 135534747 6479403 0.04780621311817552 0.43093495221116573 chr11 135006516 5312681 0.03935129323683903 0.29980780362559706 chr12 133851895 6011920 0.04491471712074006 0.24858361650545285 chr13 115169878 4000229 0.03473329198108554 0.21305474894849813 chr14 107349540 3582428 0.033371619477829156 0.21763678665660027 chr15 102531392 3978683 0.03880453510277126 0.22631018494016608 chr16 90354753 4097845 0.045352843806678325 0.2644376229321443 chr17 81195210 3657624 0.04504728788804167 0.28064017882469167 chr18 78077248 3463916 0.044365241971643266 0.48264496860716066 chr19 59128983 3928589 0.06644100406732854 0.5596775735512673 chr20 63025520 3748687 0.05947887458921402 0.29780173348519706 chr21 48129895 1775842 0.03689686004924798 0.287652294324113 chr22 51304566 998222 0.019456786750715327 0.161812101081379 chrMT 16571 41245 2.488986784140969 2.374439094853731 chrX 155270560 7296538 0.04699241118213266 0.27491185893976683 chrY 59373566 473947 0.007982458052123735 0.26647497786104324