BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231720.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 = 813,376 number of mapped reads = 386,052 (47.46%) number of supplementary alignments = 1,597 (0.2%) number of secondary alignments = 0 number of mapped bases = 23,652,911 bp number of sequenced bases = 23,636,386 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,786 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8517 >>>>>>> ACTG content number of A's = 6,411,873 bp (27.13%) number of C's = 3,832,900 bp (16.22%) number of T's = 7,865,135 bp (33.28%) number of G's = 5,519,263 bp (23.35%) number of N's = 7,215 bp (0.03%) GC percentage = 39.57% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 274,491 number of insertions = 2,023 mapped reads with insertion percentage = 0.52% number of deletions = 9,283 mapped reads with deletion percentage = 2.37% homopolymer indels = 47.22% >>>>>>> Coverage mean coverageData = 0.0076X std coverageData = 0.113X There is a 0.7% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% 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 1984881 0.00796339440213471 0.1283663403771372 chr2 243199373 1732026 0.007121835795193435 0.10951530410947936 chr3 198022430 1997570 0.010087594622487967 0.10944954973836496 chr4 191154276 1261848 0.006601202057337185 0.0884642673674326 chr5 180915260 1413531 0.007813221504918933 0.09604025944437762 chr6 171115067 1506793 0.008805729538708593 0.10784302932038319 chr7 159138663 1453734 0.009135014537604857 0.13191126350653187 chr8 146364022 1207835 0.008252267076946 0.2241378340474437 chr9 141213431 968538 0.006858681877080092 0.1014181013372772 chr10 135534747 1167190 0.008611739984286096 0.106534171571124 chr11 135006516 1136932 0.008421312049856912 0.1114781832588048 chr12 133851895 938625 0.007012414728980863 0.08973684480779383 chr13 115169878 959302 0.008329452254868239 0.09913528410513273 chr14 107349540 935458 0.008714131425248772 0.1017302729811435 chr15 102531392 553763 0.0054009117519832365 0.07997247257237347 chr16 90354753 597226 0.006609790632707501 0.08940737793614963 chr17 81195210 555745 0.006844554007557835 0.08974828134914856 chr18 78077248 548238 0.007021738266184792 0.13537055193886186 chr19 59128983 510890 0.00864026360811922 0.1105228794473528 chr20 63025520 512464 0.008131055483556502 0.09924960121056788 chr21 48129895 355401 0.0073842047650426 0.09276346139481739 chr22 51304566 209866 0.004090591079164377 0.06774622627977876 chrMT 16571 14290 0.8623498883591817 1.1049143708888052 chrX 155270560 1042034 0.006711085475572446 0.09100086937630514 chrY 59373566 88731 0.001494452935503318 0.043164762750369116