BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716723.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 = 1,071,771 number of mapped reads = 975,566 (91.02%) number of supplementary alignments = 4,412 (0.41%) number of secondary alignments = 0 number of mapped bases = 56,445,391 bp number of sequenced bases = 56,428,956 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,728 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1467 >>>>>>> ACTG content number of A's = 13,793,840 bp (24.44%) number of C's = 11,224,307 bp (19.89%) number of T's = 17,464,824 bp (30.95%) number of G's = 13,945,181 bp (24.71%) number of N's = 804 bp (0%) GC percentage = 44.6% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 283,417 number of insertions = 3,616 mapped reads with insertion percentage = 0.37% number of deletions = 10,583 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.98% >>>>>>> Coverage mean coverageData = 0.0182X std coverageData = 0.2012X There is a 1.68% of reference with a coverageData >= 1X There is a 0.1% 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 4305833 0.017275114431911487 0.25841886060503133 chr2 243199373 5638620 0.023185174905858003 0.2499340212363968 chr3 198022430 4333040 0.02188156159885524 0.16431964833255672 chr4 191154276 3145551 0.016455561789263874 0.14190888587173323 chr5 180915260 2864549 0.015833650516822076 0.1332286046652421 chr6 171115067 3190720 0.018646633846685166 0.1526903005902736 chr7 159138663 3594136 0.02258493273881533 0.4137904660095417 chr8 146364022 4066740 0.027785106916507117 0.21972052180197518 chr9 141213431 1886810 0.013361406111575888 0.13686311958727487 chr10 135534747 2306358 0.017016728558913383 0.2563711458157376 chr11 135006516 1958721 0.014508344175032262 0.14910343851334848 chr12 133851895 2711208 0.020255282900552136 0.1675500665732511 chr13 115169878 1503418 0.013053916754170738 0.12083489373976068 chr14 107349540 1871459 0.01743332109294553 0.1409867932059006 chr15 102531392 1372250 0.013383705938567575 0.12623340202628164 chr16 90354753 1816051 0.020099119744148932 0.15590877795212185 chr17 81195210 2478830 0.030529263979981087 0.1897588288108203 chr18 78077248 1347956 0.017264389236669817 0.21076452554335331 chr19 59128983 1189191 0.02011181217170605 0.25126329785922075 chr20 63025520 1186199 0.01882093158453909 0.15198848446931282 chr21 48129895 577500 0.011998779552708352 0.1179142345989101 chr22 51304566 917041 0.01787445195423737 0.14125581326768238 chrMT 16571 72332 4.364974956248869 3.1984177905919027 chrX 155270560 1988226 0.012804912921032809 0.13430452109441263 chrY 59373566 122652 0.0020657677862906195 0.060866181530603795