BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524995.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 = 1,405,635 number of mapped reads = 1,282,640 (91.25%) number of supplementary alignments = 4,525 (0.32%) number of secondary alignments = 0 number of mapped bases = 74,433,133 bp number of sequenced bases = 74,408,708 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,650 duplication rate = 2.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9988 >>>>>>> ACTG content number of A's = 18,317,292 bp (24.62%) number of C's = 13,843,854 bp (18.61%) number of T's = 24,001,415 bp (32.26%) number of G's = 18,245,318 bp (24.52%) number of N's = 829 bp (0%) GC percentage = 43.13% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 364,635 number of insertions = 5,565 mapped reads with insertion percentage = 0.43% number of deletions = 14,629 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.07% >>>>>>> Coverage mean coverageData = 0.024X std coverageData = 0.2315X There is a 2.21% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 7816677 0.03136071223670091 0.44040878947308804 chr2 243199373 7076496 0.029097509227542295 0.26392809767380065 chr3 198022430 4073139 0.020569078967468485 0.15331946363824775 chr4 191154276 4755618 0.024878428563115167 0.18029969692438666 chr5 180915260 3243880 0.017930383539785422 0.14605493531900854 chr6 171115067 4950651 0.028931707106773945 0.24156784489283484 chr7 159138663 4653811 0.029243748264995793 0.28177204716490434 chr8 146364022 4354786 0.02975311788029438 0.23575649049889202 chr9 141213431 2079532 0.014726162980913622 0.17354272909155516 chr10 135534747 3755953 0.027712103966962803 0.2243952302796584 chr11 135006516 3104395 0.022994408655060767 0.20680317209930218 chr12 133851895 3990950 0.029816163603810016 0.18457680561021417 chr13 115169878 2045535 0.017761024284492166 0.1436434633336873 chr14 107349540 1700876 0.01584427841982369 0.1377986142266137 chr15 102531392 2061973 0.020110650599574422 0.15672052612088677 chr16 90354753 2370401 0.026234380829971392 0.17864131266344588 chr17 81195210 1916592 0.0236047422009254 0.21004977217174023 chr18 78077248 1453499 0.018616165877157965 0.2790162868875821 chr19 59128983 1825378 0.03087112118941738 0.2785429180203133 chr20 63025520 1809662 0.028713162541142066 0.1813543446426968 chr21 48129895 1076106 0.022358369990210864 0.16976655992939022 chr22 51304566 1007100 0.019629831777545882 0.14859064375417252 chrMT 16571 4269 0.2576187315189186 0.5806624557547413 chrX 155270560 3097137 0.019946711082899422 0.1686554268103438 chrY 59373566 208717 0.00351531858470485 0.09654551239361292