BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716717.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 = 552,830 number of mapped reads = 521,772 (94.38%) number of supplementary alignments = 10,963 (1.98%) number of secondary alignments = 0 number of mapped bases = 40,564,410 bp number of sequenced bases = 40,548,655 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,875 duplication rate = 1.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0335 >>>>>>> ACTG content number of A's = 9,824,514 bp (24.23%) number of C's = 8,089,139 bp (19.95%) number of T's = 12,332,154 bp (30.41%) number of G's = 10,301,367 bp (25.4%) number of N's = 1,481 bp (0%) GC percentage = 45.35% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 264,879 number of insertions = 3,205 mapped reads with insertion percentage = 0.6% number of deletions = 7,442 mapped reads with deletion percentage = 1.4% homopolymer indels = 39.16% >>>>>>> Coverage mean coverageData = 0.0131X std coverageData = 0.1493X There is a 1.2% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5098350 0.02045471333048354 0.24551891042804466 chr2 243199373 3696602 0.015199882937198197 0.1602908179344874 chr3 198022430 2046947 0.010336945163232266 0.10808144881323897 chr4 191154276 1878705 0.009828213311848697 0.13244522496562244 chr5 180915260 2050586 0.011334510974917207 0.11380178415894053 chr6 171115067 2422321 0.01415609415622062 0.13017117156408056 chr7 159138663 2509479 0.015769134619410496 0.17876897888279478 chr8 146364022 2971802 0.020304183769970466 0.18691665089164203 chr9 141213431 1262434 0.008939900341349259 0.11213427406747861 chr10 135534747 2284618 0.016856326887156103 0.200612101826157 chr11 135006516 1212255 0.008979233269007549 0.11769339304696202 chr12 133851895 1450399 0.010835849578371677 0.11035191183267028 chr13 115169878 776142 0.006739105862385302 0.08654961008980656 chr14 107349540 744083 0.006931403711650744 0.09045098639967679 chr15 102531392 831372 0.008108463015892733 0.0951050119780095 chr16 90354753 1223861 0.013545064972951671 0.1272945333391003 chr17 81195210 1072890 0.013213710513218698 0.12940347774996921 chr18 78077248 1142169 0.014628704638770055 0.16210159879371797 chr19 59128983 844398 0.014280610914616949 0.17900559407900798 chr20 63025520 1086309 0.017236018044753935 0.14447500710476935 chr21 48129895 665827 0.01383395912249549 0.13382307622186582 chr22 51304566 626216 0.012205853178837923 0.1195354201895358 chrMT 16571 3401 0.20523806650171988 0.5158161891087687 chrX 155270560 2520351 0.016231995299044455 0.13790457235795034 chrY 59373566 142893 0.0024066770724197363 0.09288946424222427