BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237839.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,205,703 number of mapped reads = 1,876,115 (85.06%) number of supplementary alignments = 11,138 (0.5%) number of secondary alignments = 0 number of mapped bases = 120,182,254 bp number of sequenced bases = 120,134,547 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,432 duplication rate = 1.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6254 >>>>>>> ACTG content number of A's = 33,401,102 bp (27.8%) number of C's = 21,936,449 bp (18.26%) number of T's = 36,285,680 bp (30.2%) number of G's = 28,402,975 bp (23.64%) number of N's = 108,341 bp (0.09%) GC percentage = 41.9% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 951,269 number of insertions = 10,896 mapped reads with insertion percentage = 0.58% number of deletions = 28,068 mapped reads with deletion percentage = 1.48% homopolymer indels = 45.99% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.3592X There is a 3.52% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11194663 0.044913280276240516 0.5736871982705617 chr2 243199373 10612133 0.043635527793897726 0.39300186892457034 chr3 198022430 8481312 0.04283005718089612 0.2277646080800432 chr4 191154276 5205728 0.02723312346933845 0.2517209931622608 chr5 180915260 6457095 0.03569126783445465 0.20328510381017176 chr6 171115067 7316530 0.042757953044543995 0.27892100239254414 chr7 159138663 6769805 0.0425402907903028 0.4895674122679778 chr8 146364022 6273689 0.042863600728326526 0.3324590922164843 chr9 141213431 6100626 0.04320145723249228 0.3884689674336077 chr10 135534747 7338221 0.05414272843258416 0.5637839219104528 chr11 135006516 5356791 0.03967801820765451 0.324475155511506 chr12 133851895 5570143 0.04161422593232617 0.22578048753026816 chr13 115169878 4238895 0.036805587308167506 0.20235250995851134 chr14 107349540 2955579 0.027532293105308137 0.2413134535753821 chr15 102531392 2457663 0.02396985890916218 0.164937555476496 chr16 90354753 3085040 0.03414363824335838 0.2654163939769654 chr17 81195210 2903122 0.03575484317363056 0.2642958462798606 chr18 78077248 2114467 0.02708173064706379 0.6905913182475172 chr19 59128983 2543503 0.043016180406823507 0.4254029971505105 chr20 63025520 2309295 0.036640633825789935 0.22648486822027658 chr21 48129895 1913334 0.039753546106842744 0.2726251447866913 chr22 51304566 1099436 0.02142959361550783 0.15448896278187205 chrMT 16571 36600 2.208677810633034 1.8287413898410727 chrX 155270560 7446749 0.04795982573901968 0.27208187108322623 chrY 59373566 401835 0.006767910824153631 0.23176265449133326