BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251056.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 1,654,812 number of mapped reads = 1,509,074 (91.19%) number of supplementary alignments = 48,702 (2.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 757,247 number of mapped paired reads (second in pair) = 751,827 number of mapped paired reads (both in pair) = 1,498,836 number of mapped paired reads (singletons) = 10,238 number of mapped bases = 185,435,864 bp number of sequenced bases = 185,259,650 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 245,612 duplication rate = 14.44% >>>>>>> Insert size mean insert size = 104,874.3913 std insert size = 3,105,674.4616 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 53.0779 >>>>>>> ACTG content number of A's = 54,898,505 bp (29.63%) number of C's = 37,451,137 bp (20.22%) number of T's = 54,798,653 bp (29.58%) number of G's = 38,104,800 bp (20.57%) number of N's = 6,555 bp (0%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,421,462 number of insertions = 32,601 mapped reads with insertion percentage = 2.02% number of deletions = 84,381 mapped reads with deletion percentage = 5.35% homopolymer indels = 43.88% >>>>>>> Coverage mean coverageData = 0.0599X std coverageData = 0.695X There is a 3.75% of reference with a coverageData >= 1X There is a 1.44% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.04% 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 0.01% 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 15214966 0.06104284089226 1.3394734814158906 chr2 243199373 16731090 0.06879577769306174 1.0634813032921062 chr3 198022430 12605824 0.06365856635533662 0.3621220505109449 chr4 191154276 11815569 0.06181169078320801 0.4144351440923566 chr5 180915260 10939115 0.06046540794845056 0.35714260813376764 chr6 171115067 10760248 0.06288311244970614 0.4212393454006379 chr7 159138663 9951789 0.06253533121614827 0.846682795387347 chr8 146364022 8880141 0.06067161095094804 0.5004044524529487 chr9 141213431 8361912 0.059214707416888696 1.0040166357756268 chr10 135534747 11016244 0.08127985069393312 0.8411931016114189 chr11 135006516 8388301 0.06213256403120573 0.4753789621199661 chr12 133851895 8326121 0.06220398299179851 0.36627680984279554 chr13 115169878 5506998 0.04781630488485887 0.3144612967437919 chr14 107349540 5581859 0.05199704628450201 0.3430688817108942 chr15 102531392 5555245 0.05418091856199514 0.3321446190155922 chr16 90354753 5044690 0.05583203796705637 0.6281962120111307 chr17 81195210 5332936 0.06568042622218724 0.49332509860319895 chr18 78077248 4853061 0.062157172855272766 0.817630573541534 chr19 59128983 3560657 0.06021847187867243 0.6928986414477871 chr20 63025520 3771414 0.05983947454935715 0.3615222559629203 chr21 48129895 2273538 0.04723754331897047 0.32547813732052583 chr22 51304566 2121755 0.041356065657002145 0.30678369907921454 chrMT 16571 193978 11.705871703578541 7.204642368570467 chrX 155270560 8223481 0.05296226792767412 0.3455252205769911 chrY 59373566 424932 0.007156922324658754 0.45026074115694786