BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777306.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 2,580,297 number of mapped reads = 2,349,485 (91.05%) number of supplementary alignments = 59 (0%) number of secondary alignments = 0 number of mapped bases = 119,451,456 bp number of sequenced bases = 119,401,140 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,764 duplication rate = 0.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5797 >>>>>>> ACTG content number of A's = 33,990,706 bp (28.47%) number of C's = 26,051,807 bp (21.82%) number of T's = 33,288,634 bp (27.88%) number of G's = 26,053,879 bp (21.82%) number of N's = 16,114 bp (0.01%) GC percentage = 43.64% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 649,659 number of insertions = 13,562 mapped reads with insertion percentage = 0.58% number of deletions = 42,139 mapped reads with deletion percentage = 1.79% homopolymer indels = 55.67% >>>>>>> Coverage mean coverageData = 0.0386X std coverageData = 0.2147X There is a 3.5% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 10834686 0.04346904315235387 0.23259636051819993 chr2 243199373 10161086 0.04178088896635437 0.22601018898096212 chr3 198022430 7871798 0.03975205233063749 0.21413734572965962 chr4 191154276 6092666 0.03187303013823243 0.19677028958809056 chr5 180915260 7010506 0.038750219301566934 0.2114985495585029 chr6 171115067 6582177 0.03846637888409908 0.21087773656995093 chr7 159138663 6110906 0.038399882748794995 0.21121951433217903 chr8 146364022 5957676 0.04070451138600168 0.219174042271007 chr9 141213431 5280414 0.037393142866134314 0.21240346456576994 chr10 135534747 6114535 0.04511415069081879 0.23155285759899893 chr11 135006516 6192096 0.04586516401919445 0.23457436414307672 chr12 133851895 5547816 0.04144742216761294 0.21979917173433217 chr13 115169878 3252063 0.02823709685617623 0.1801208880978307 chr14 107349540 3721037 0.034662812714428025 0.202101085317736 chr15 102531392 3944029 0.03846655081011677 0.2128285670378165 chr16 90354753 4193599 0.0464125998994209 0.23777392907897246 chr17 81195210 3978231 0.048995882885209605 0.243750694360773 chr18 78077248 3056768 0.03915056022466366 0.2194169234130775 chr19 59128983 2440435 0.041273075845055546 0.22393783497902028 chr20 63025520 3406483 0.05404926448841676 0.25432104033183783 chr21 48129895 1507252 0.03131633675909744 0.20397130301857785 chr22 51304566 2118965 0.04130168453232798 0.2255252451433135 chrMT 16571 26540 1.6015931446502927 1.7563995539983965 chrX 155270560 3432284 0.022105182077014472 0.15622965957204915 chrY 59373566 617408 0.010398701671380156 0.11431506384373635