BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173884.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 = 4,198,740 number of mapped reads = 4,085,973 (97.31%) number of supplementary alignments = 405,288 (9.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,045,817 number of mapped paired reads (second in pair) = 2,040,156 number of mapped paired reads (both in pair) = 4,014,948 number of mapped paired reads (singletons) = 71,025 number of mapped bases = 480,756,397 bp number of sequenced bases = 480,495,408 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,995,113 duplication rate = 62.29% >>>>>>> Insert size mean insert size = 690,147.8887 std insert size = 7,525,664.4511 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 52.7514 >>>>>>> ACTG content number of A's = 145,583,270 bp (30.3%) number of C's = 93,354,862 bp (19.43%) number of T's = 145,026,595 bp (30.18%) number of G's = 96,525,113 bp (20.09%) number of N's = 5,568 bp (0%) GC percentage = 39.52% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 4,825,348 number of insertions = 50,096 mapped reads with insertion percentage = 1.18% number of deletions = 107,362 mapped reads with deletion percentage = 2.57% homopolymer indels = 43.36% >>>>>>> Coverage mean coverageData = 0.1553X std coverageData = 2.3526X There is a 3.7% of reference with a coverageData >= 1X There is a 2.8% of reference with a coverageData >= 2X There is a 2.03% of reference with a coverageData >= 3X There is a 1.61% of reference with a coverageData >= 4X There is a 1.16% of reference with a coverageData >= 5X There is a 0.92% of reference with a coverageData >= 6X There is a 0.65% of reference with a coverageData >= 7X There is a 0.53% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 35521239 0.14251213841509347 1.4732904959530195 chr2 243199373 42495560 0.17473548338465494 7.00942336041157 chr3 198022430 43674473 0.2205531615787161 1.2992359192410756 chr4 191154276 24996719 0.13076725000909736 1.1709148798577849 chr5 180915260 30883275 0.17070574919992929 1.1273707418984957 chr6 171115067 27755774 0.16220531883378803 1.2280847621947315 chr7 159138663 27825353 0.17484973466190298 1.4606486416402966 chr8 146364022 29537791 0.20181046268324057 1.5525637047268057 chr9 141213431 17956072 0.1271555536385204 1.1706806216192895 chr10 135534747 25495976 0.18811394542242366 2.27100088609755 chr11 135006516 15516812 0.11493380067670216 0.9240309418668543 chr12 133851895 21820077 0.16301657141275439 1.0958765468506002 chr13 115169878 12908938 0.11208606125292588 0.9172954825038093 chr14 107349540 14374913 0.13390754166249805 0.9871201763831298 chr15 102531392 13762069 0.13422298021663454 0.9850535872247208 chr16 90354753 13883025 0.1536501903779207 1.4029990785901887 chr17 81195210 18724724 0.23061365319456653 1.4249239864816676 chr18 78077248 9148716 0.11717518527292356 1.6715899166821546 chr19 59128983 6837852 0.11564298340798454 1.2094245970824478 chr20 63025520 18451329 0.29275964720322817 1.5930928858734141 chr21 48129895 4803747 0.09980796758438804 0.9357069454266039 chr22 51304566 3499500 0.06821030315313456 0.6883663011098584 chrMT 16571 1980801 119.5341862289542 87.7695508049085 chrX 155270560 18026923 0.11610007074103423 0.9231986651655828 chrY 59373566 874739 0.014732802136223383 0.5956367951530762