BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163164.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 = 63,023,376 number of mapped reads = 60,869,083 (96.58%) number of supplementary alignments = 677,506 (1.08%) number of secondary alignments = 0 number of mapped bases = 6,052,329,523 bp number of sequenced bases = 6,051,181,902 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,658,692 duplication rate = 48.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4051 >>>>>>> ACTG content number of A's = 1,569,172,491 bp (25.93%) number of C's = 1,458,983,883 bp (24.11%) number of T's = 1,593,061,356 bp (26.33%) number of G's = 1,427,188,712 bp (23.59%) number of N's = 2,775,460 bp (0.05%) GC percentage = 47.7% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 54,145,328 number of insertions = 437,015 mapped reads with insertion percentage = 0.71% number of deletions = 569,099 mapped reads with deletion percentage = 0.92% homopolymer indels = 45.62% >>>>>>> Coverage mean coverageData = 1.9551X std coverageData = 18.6383X There is a 7.69% of reference with a coverageData >= 1X There is a 5.71% of reference with a coverageData >= 2X There is a 4.75% of reference with a coverageData >= 3X There is a 4.28% of reference with a coverageData >= 4X There is a 3.94% of reference with a coverageData >= 5X There is a 3.7% of reference with a coverageData >= 6X There is a 3.49% of reference with a coverageData >= 7X There is a 3.33% of reference with a coverageData >= 8X There is a 3.18% of reference with a coverageData >= 9X There is a 3.05% of reference with a coverageData >= 10X There is a 2.93% of reference with a coverageData >= 11X There is a 2.82% of reference with a coverageData >= 12X There is a 2.72% of reference with a coverageData >= 13X There is a 2.63% of reference with a coverageData >= 14X There is a 2.55% of reference with a coverageData >= 15X There is a 2.47% of reference with a coverageData >= 16X There is a 2.39% of reference with a coverageData >= 17X There is a 2.32% of reference with a coverageData >= 18X There is a 2.25% of reference with a coverageData >= 19X There is a 2.19% of reference with a coverageData >= 20X There is a 2.13% of reference with a coverageData >= 21X There is a 2.07% of reference with a coverageData >= 22X There is a 2.02% of reference with a coverageData >= 23X There is a 1.96% of reference with a coverageData >= 24X There is a 1.91% of reference with a coverageData >= 25X There is a 1.86% of reference with a coverageData >= 26X There is a 1.82% of reference with a coverageData >= 27X There is a 1.77% of reference with a coverageData >= 28X There is a 1.73% of reference with a coverageData >= 29X There is a 1.69% of reference with a coverageData >= 30X There is a 1.65% of reference with a coverageData >= 31X There is a 1.61% of reference with a coverageData >= 32X There is a 1.57% of reference with a coverageData >= 33X There is a 1.53% of reference with a coverageData >= 34X There is a 1.5% of reference with a coverageData >= 35X There is a 1.46% of reference with a coverageData >= 36X There is a 1.43% of reference with a coverageData >= 37X There is a 1.4% of reference with a coverageData >= 38X There is a 1.37% of reference with a coverageData >= 39X There is a 1.34% of reference with a coverageData >= 40X There is a 1.31% of reference with a coverageData >= 41X There is a 1.28% of reference with a coverageData >= 42X There is a 1.26% of reference with a coverageData >= 43X There is a 1.23% of reference with a coverageData >= 44X There is a 1.2% of reference with a coverageData >= 45X There is a 1.18% of reference with a coverageData >= 46X There is a 1.16% of reference with a coverageData >= 47X There is a 1.13% of reference with a coverageData >= 48X There is a 1.11% of reference with a coverageData >= 49X There is a 1.09% of reference with a coverageData >= 50X There is a 1.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 684158937 2.7448635203199756 22.534505308855053 chr2 243199373 398515290 1.638636173622043 15.28753921480079 chr3 198022430 295171901 1.4905983175744284 13.41753094712743 chr4 191154276 213822907 1.118588145001789 13.778912458648927 chr5 180915260 291631616 1.6119790889944827 21.501886733729837 chr6 171115067 291801057 1.7052914282527791 15.657337455093709 chr7 159138663 334297794 2.1006698667563897 20.534161198389697 chr8 146364022 267027990 1.8244100315854945 28.92633627648091 chr9 141213431 248265377 1.7580861483352812 15.38558497200874 chr10 135534747 251295430 1.854103361405913 18.212233331978123 chr11 135006516 304065539 2.2522286183579463 17.65487938330046 chr12 133851895 295593403 2.2083617344379025 16.95673493803269 chr13 115169878 112355640 0.9755644613950186 11.097424967810849 chr14 107349540 167973159 1.564731055205267 13.551143408534402 chr15 102531392 263272749 2.5677282231767613 20.013829507153588 chr16 90354753 234507274 2.595406065688653 19.337099040787034 chr17 81195210 345204961 4.251543422327499 27.43914454332212 chr18 78077248 98901569 1.2667143314272553 12.398877258392524 chr19 59128983 359453954 6.079149949188201 34.11723957682983 chr20 63025520 128874683 2.0448015819623544 16.714173266859632 chr21 48129895 69329322 1.4404627726696682 15.978511123553192 chr22 51304566 121445337 2.3671448073452175 17.859934053896342 chrMT 16571 8045 0.48548669362138674 0.8844000506517705 chrX 155270560 268579424 1.7297511131537104 16.22373981619921 chrY 59373566 6776165 0.1141276405732477 9.856848047212756