BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084392.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,336 number of mapped reads = 1,183 (35.46%) number of supplementary alignments = 4 (0.12%) number of secondary alignments = 0 number of mapped bases = 78,211 bp number of sequenced bases = 78,179 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 0 duplication rate = 0% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.4219 >>>>>>> ACTG content number of A's = 22,323 bp (28.55%) number of C's = 14,695 bp (18.8%) number of T's = 23,724 bp (30.35%) number of G's = 17,303 bp (22.13%) number of N's = 134 bp (0.17%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 944 number of insertions = 10 mapped reads with insertion percentage = 0.85% number of deletions = 15 mapped reads with deletion percentage = 1.27% homopolymer indels = 40% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.005X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 6685 2.6820394561825385E-5 0.005176059558383328 chr2 243199373 8944 3.677641060365727E-5 0.0060611924690501685 chr3 198022430 4412 2.228030430694139E-5 0.00472870033123885 chr4 191154276 4469 2.337902187445705E-5 0.004834588313790115 chr5 180915260 3810 2.105958336516223E-5 0.004589023845994997 chr6 171115067 3556 2.078133774157947E-5 0.004558607888114654 chr7 159138663 4028 2.531125952717097E-5 0.0050309659974315185 chr8 146364022 3837 2.6215458878275427E-5 0.0051200362916673965 chr9 141213431 2804 1.9856468185381036E-5 0.004456015474171094 chr10 135534747 5953 4.392231609802614E-5 0.0066266891729229935 chr11 135006516 4020 2.9776340573072783E-5 0.00545397355214328 chr12 133851895 3588 2.680574675464998E-5 0.005177357260861076 chr13 115169878 2087 1.8121057660580312E-5 0.004256844992227175 chr14 107349540 2178 2.0288861973698256E-5 0.004504270233431612 chr15 102531392 1860 1.8140785604471263E-5 0.004256871034340269 chr16 90354753 2340 2.5897918175925952E-5 0.005088933824855665 chr17 81195210 1789 2.20333194532042E-5 0.004693914569529154 chr18 78077248 2106 2.6973286763385923E-5 0.005349014979385026 chr19 59128983 1849 3.127062070389406E-5 0.005584360951893463 chr20 63025520 1462 2.3196952599518418E-5 0.0048162656177694885 chr21 48129895 710 1.4751746289909837E-5 0.00384077188542762 chr22 51304566 957 1.8653310506515152E-5 0.0043166505354437276 chrMT 16571 0 0.0 0.0 chrX 155270560 4617 2.973519255678604E-5 0.005452917418695212 chrY 59373566 150 2.526376805462552E-6 0.001578824109586651