BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472657.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 162,530 number of mapped reads = 160,876 (98.98%) number of supplementary alignments = 944 (0.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 80,738 number of mapped paired reads (second in pair) = 80,138 number of mapped paired reads (both in pair) = 159,772 number of mapped paired reads (singletons) = 1,104 number of mapped bases = 15,829,543 bp number of sequenced bases = 15,827,371 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,245 duplication rate = 21.07% >>>>>>> Insert size mean insert size = 18,374.1138 std insert size = 1,193,090.371 median insert size = 215 >>>>>>> Mapping quality mean mapping quality = 54.5354 >>>>>>> ACTG content number of A's = 4,307,433 bp (27.22%) number of C's = 3,631,115 bp (22.94%) number of T's = 4,308,662 bp (27.22%) number of G's = 3,576,581 bp (22.6%) number of N's = 3,580 bp (0.02%) GC percentage = 45.54% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 98,286 number of insertions = 917 mapped reads with insertion percentage = 0.56% number of deletions = 838 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.58% >>>>>>> Coverage mean coverageData = 0.0051X std coverageData = 0.2187X There is a 0.18% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 0.01% 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 1568745 0.006293845903798169 0.29978624118921077 chr2 243199373 1193660 0.004908154101203213 0.23122985642012983 chr3 198022430 1401318 0.007076561983407637 0.20237367633226333 chr4 191154276 417225 0.0021826610878429944 0.11521497698845097 chr5 180915260 631594 0.003491104067174875 0.1733371749250244 chr6 171115067 1379031 0.008059085761278988 0.27201472998163434 chr7 159138663 1047186 0.006580336797224444 0.2559219440375609 chr8 146364022 704134 0.004810840740629552 0.18600510897587633 chr9 141213431 1339513 0.009485733690586414 0.3459866622140662 chr10 135534747 369162 0.0027237443398924117 0.13911174102826576 chr11 135006516 432993 0.003207200754665797 0.13575548255098568 chr12 133851895 541698 0.004046995375000108 0.14064996416732425 chr13 115169878 511575 0.004441916661577084 0.22230454090202173 chr14 107349540 262420 0.0024445377222855357 0.1684414091009294 chr15 102531392 137314 0.001339238620694821 0.07559621524581257 chr16 90354753 1041338 0.011524994152770248 0.41187039284897375 chr17 81195210 558465 0.006878053520644876 0.20650803899542117 chr18 78077248 56112 7.186728712569378E-4 0.04090771682620447 chr19 59128983 374110 0.00632701563630817 0.19662687538340348 chr20 63025520 725245 0.011507164082105153 0.2999338737028255 chr21 48129895 97072 0.0020168753744424332 0.12503362654737057 chr22 51304566 170652 0.0033262536515755734 0.18680519775958396 chrMT 16571 200 0.012069277653732424 0.10919528465391506 chrX 155270560 857249 0.005521001534353969 0.17852796941444066 chrY 59373566 11532 1.94227848803961E-4 0.018757742727536768