BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173882.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,178,126 number of mapped reads = 2,126,751 (97.64%) number of supplementary alignments = 200,975 (9.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,065,335 number of mapped paired reads (second in pair) = 1,061,416 number of mapped paired reads (both in pair) = 2,094,896 number of mapped paired reads (singletons) = 31,855 number of mapped bases = 252,341,163 bp number of sequenced bases = 252,195,410 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,623,491 duplication rate = 63.86% >>>>>>> Insert size mean insert size = 889,644.9972 std insert size = 8,743,086.4523 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 53.1771 >>>>>>> ACTG content number of A's = 76,751,604 bp (30.43%) number of C's = 48,578,476 bp (19.26%) number of T's = 76,545,343 bp (30.35%) number of G's = 50,316,654 bp (19.95%) number of N's = 3,333 bp (0%) GC percentage = 39.21% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 2,517,652 number of insertions = 28,027 mapped reads with insertion percentage = 1.27% number of deletions = 59,857 mapped reads with deletion percentage = 2.74% homopolymer indels = 42.62% >>>>>>> Coverage mean coverageData = 0.0815X std coverageData = 1.3063X There is a 1.8% of reference with a coverageData >= 1X There is a 1.38% of reference with a coverageData >= 2X There is a 1.03% of reference with a coverageData >= 3X There is a 0.84% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.51% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 19128285 0.07674317890666359 0.9622338519825542 chr2 243199373 21724579 0.08932826895075918 3.4652575163764756 chr3 198022430 19464673 0.09829529412400403 0.9176629098449752 chr4 191154276 18229198 0.09536379923826553 1.0074208519028423 chr5 180915260 15677851 0.08665853284018164 0.855617887927803 chr6 171115067 14575781 0.08518116642528037 0.8818075402126856 chr7 159138663 15136578 0.09511565395016545 1.0319489368181607 chr8 146364022 12598160 0.08607415830647233 1.062636058335136 chr9 141213431 10032303 0.07104354684222636 0.9152550860570196 chr10 135534747 11845238 0.08739631911512699 1.143179123797896 chr11 135006516 12260770 0.09081613512639641 0.8787117654361258 chr12 133851895 11060403 0.0826316504521658 0.8293622435735031 chr13 115169878 9897952 0.08594219401708492 0.8631796610319317 chr14 107349540 7213109 0.06719273319662106 0.7426728918062685 chr15 102531392 6826299 0.066577648726353 0.7318975536447191 chr16 90354753 7372582 0.0815959510176515 0.8820806249842194 chr17 81195210 7082821 0.08723200543480336 0.9107473516841462 chr18 78077248 6709219 0.08593052613739664 1.1328334085017426 chr19 59128983 4315661 0.07298723537998278 0.805807223783339 chr20 63025520 5808570 0.09216219080778706 0.8657361982191796 chr21 48129895 3434553 0.0713600767257024 0.8856801213321349 chr22 51304566 2820455 0.054974736556586405 0.6847603456926656 chrMT 16571 378385 22.834168125037717 20.852410657973923 chrX 155270560 6928262 0.044620577139671554 0.6051072387378497 chrY 59373566 1819476 0.030644546429971883 0.5870982272349274