BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818770.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,053,901 number of mapped reads = 1,027,811 (97.52%) number of supplementary alignments = 7,807 (0.74%) number of secondary alignments = 0 number of mapped bases = 69,841,862 bp number of sequenced bases = 69,812,950 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 495,930 duplication rate = 40.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.01 >>>>>>> ACTG content number of A's = 20,132,801 bp (28.84%) number of C's = 16,488,313 bp (23.62%) number of T's = 18,842,965 bp (26.99%) number of G's = 14,344,465 bp (20.55%) number of N's = 4,406 bp (0.01%) GC percentage = 44.16% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 358,586 number of insertions = 7,917 mapped reads with insertion percentage = 0.76% number of deletions = 17,967 mapped reads with deletion percentage = 1.73% homopolymer indels = 41.44% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.3342X There is a 1% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 6088578 0.024427533923777063 0.3807042482748101 chr2 243199373 6144684 0.0252660355337347 0.4843620036364636 chr3 198022430 4713048 0.023800576530648574 0.29562407550145653 chr4 191154276 4298695 0.022488092288346195 0.308086850124754 chr5 180915260 4140680 0.02288740043266665 0.2922844227646464 chr6 171115067 4086551 0.023881888787736033 0.3032203163350385 chr7 159138663 3684076 0.023150100236797894 0.31339655578113174 chr8 146364022 3420891 0.0233724856235503 0.3006331029524468 chr9 141213431 3026270 0.021430468607479696 0.2896638729242795 chr10 135534747 3382805 0.024958950194520966 0.35969559975628196 chr11 135006516 3415347 0.025297645633637417 0.3182854543379343 chr12 133851895 3121203 0.023318332549569058 0.3125299529103709 chr13 115169878 2098270 0.018218913108512626 0.26303121146732145 chr14 107349540 2224791 0.020724737153042294 0.29526150272024954 chr15 102531392 2178576 0.021247892547874507 0.2838782104535885 chr16 90354753 2179897 0.024125980400831817 0.39058748129781334 chr17 81195210 2151121 0.02649320076886309 0.33015848696317485 chr18 78077248 1781657 0.02281915725308351 0.33193791811295004 chr19 59128983 1618067 0.02736504025445525 0.3766733274573436 chr20 63025520 1542461 0.024473594188512842 0.31623726798689583 chr21 48129895 910765 0.018923062267224976 0.2725342018483139 chr22 51304566 969975 0.018906211973413828 0.2931448332124814 chrMT 16571 113292 6.836763019733269 8.123407807898955 chrX 155270560 1981546 0.012761891243259507 0.22050785991680943 chrY 59373566 568616 0.009576921824099296 0.4501345243410005