BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695954.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 19,159,388 number of mapped reads = 18,998,492 (99.16%) number of supplementary alignments = 245,349 (1.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,544,764 number of mapped paired reads (second in pair) = 9,453,728 number of mapped paired reads (both in pair) = 18,879,106 number of mapped paired reads (singletons) = 119,386 number of mapped bases = 1,881,189,675 bp number of sequenced bases = 1,880,779,418 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 304,938 duplication rate = 1.43% >>>>>>> Insert size mean insert size = 80,794.4658 std insert size = 2,740,997.4967 median insert size = 317 >>>>>>> Mapping quality mean mapping quality = 53.8338 >>>>>>> ACTG content number of A's = 555,616,138 bp (29.54%) number of C's = 380,608,629 bp (20.24%) number of T's = 553,262,559 bp (29.42%) number of G's = 390,485,496 bp (20.76%) number of N's = 806,596 bp (0.04%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 12,996,908 number of insertions = 187,138 mapped reads with insertion percentage = 0.97% number of deletions = 176,263 mapped reads with deletion percentage = 0.91% homopolymer indels = 45.01% >>>>>>> Coverage mean coverageData = 0.6077X std coverageData = 1.074X There is a 38.41% of reference with a coverageData >= 1X There is a 14.09% of reference with a coverageData >= 2X There is a 5.02% of reference with a coverageData >= 3X There is a 1.82% of reference with a coverageData >= 4X There is a 0.69% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 157052185 0.6300974672396102 1.1075962261992545 chr2 243199373 190510208 0.7833499143108399 1.3278563477908991 chr3 198022430 130544764 0.6592423090656953 0.9964360237606849 chr4 191154276 128774187 0.6736662642064046 1.1304108456015785 chr5 180915260 113703936 0.6284927871756092 0.9614365496981188 chr6 171115067 122547760 0.7161716507407264 1.0747533255876467 chr7 159138663 97680527 0.6138076389393821 0.9745373823559755 chr8 146364022 98882075 0.6755900367373069 1.0189501917688029 chr9 141213431 76447445 0.5413610055264503 0.993979481673325 chr10 135534747 82225343 0.6066735270476433 1.0536262869305493 chr11 135006516 87814480 0.650446234758032 1.0134025292145754 chr12 133851895 86038901 0.642791803582609 0.995090217682553 chr13 115169878 60844027 0.5282980937081483 0.9171253977045564 chr14 107349540 58550685 0.545420921226118 0.951272193245131 chr15 102531392 58936239 0.5748116537811171 0.9949170083418033 chr16 90354753 46331369 0.5127717962994155 1.093843832648535 chr17 81195210 44690205 0.5504044511985374 0.9863599218787362 chr18 78077248 52605356 0.6737603763903154 1.1091145061424037 chr19 59128983 27037846 0.45726891666646796 0.8845159413054887 chr20 63025520 36872989 0.5850485485879371 0.9875880188819768 chr21 48129895 26115979 0.5426145018600186 1.3429348352362962 chr22 51304566 20024047 0.39029756142952265 0.8359305258654677 chrMT 16571 1673340 100.98002534548307 29.464025576383623 chrX 155270560 63669954 0.41005812048336787 0.7749139411900713 chrY 59373566 11615828 0.1956397229029498 0.8890076532474565