BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506343.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 6,964,400 number of mapped reads = 5,300,942 (76.11%) number of supplementary alignments = 88,141 (1.27%) number of secondary alignments = 0 number of mapped bases = 412,998,057 bp number of sequenced bases = 412,819,280 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 688,580 duplication rate = 9.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3371 >>>>>>> ACTG content number of A's = 119,020,241 bp (28.83%) number of C's = 76,297,687 bp (18.48%) number of T's = 113,775,794 bp (27.56%) number of G's = 103,622,103 bp (25.1%) number of N's = 103,455 bp (0.03%) GC percentage = 43.58% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 2,996,175 number of insertions = 37,212 mapped reads with insertion percentage = 0.68% number of deletions = 87,799 mapped reads with deletion percentage = 1.62% homopolymer indels = 43.98% >>>>>>> Coverage mean coverageData = 0.1334X std coverageData = 0.8304X There is a 8.28% of reference with a coverageData >= 1X There is a 2.72% of reference with a coverageData >= 2X There is a 1.08% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.05% 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 0.01% 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 29992704 0.12033151163141936 1.1785872067148484 chr2 243199373 32859309 0.1351126386333241 0.9237765934854173 chr3 198022430 25785069 0.13021287032989143 0.5381191920248873 chr4 191154276 26707552 0.13971726167402082 0.905823256357889 chr5 180915260 31884012 0.17623727263250208 0.6452824733559231 chr6 171115067 15144899 0.08850710381920956 0.4709964438464446 chr7 159138663 20659760 0.1298223801214165 0.9212607247653489 chr8 146364022 25911104 0.17703192113701274 1.1993556888781083 chr9 141213431 11825164 0.08373965504740126 0.719577353000737 chr10 135534747 24102449 0.17783224991005442 1.0716495443550231 chr11 135006516 17567254 0.13012152687504358 0.7673682217352691 chr12 133851895 17765931 0.1327282740375099 0.5548723235141818 chr13 115169878 7850138 0.06816138157235871 0.3846800382132594 chr14 107349540 11872540 0.11059702724389876 0.5468502833763288 chr15 102531392 14928081 0.14559522414364567 0.6006973236137937 chr16 90354753 15180408 0.16800895908597083 0.850931519291465 chr17 81195210 10876608 0.13395627648478278 0.6308603591067975 chr18 78077248 7294982 0.09343287816701736 1.1310450093009805 chr19 59128983 10357632 0.1751701361073638 1.0195906557229428 chr20 63025520 10694406 0.1696837408084852 0.6940489323471067 chr21 48129895 6996478 0.1453665751815997 0.8182709814526208 chr22 51304566 5024989 0.09794428433523832 0.4919927309414795 chrMT 16571 47668 2.876591635990586 2.5523895244160553 chrX 155270560 30110970 0.1939258156858583 0.7403881175753407 chrY 59373566 1557950 0.026239791627135887 0.906401062915876