BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16328249.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 427,706,482 number of mapped reads = 403,596,223 (94.36%) number of supplementary alignments = 17,915,701 (4.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 203,067,335 number of mapped paired reads (second in pair) = 200,528,888 number of mapped paired reads (both in pair) = 400,026,962 number of mapped paired reads (singletons) = 3,569,261 number of mapped bases = 55,889,182,317 bp number of sequenced bases = 55,841,255,026 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 152,122,475 duplication rate = 32.66% >>>>>>> Insert size mean insert size = 153,528.8094 std insert size = 3,803,003.4471 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 53.7682 >>>>>>> ACTG content number of A's = 16,117,849,412 bp (28.86%) number of C's = 11,776,472,250 bp (21.09%) number of T's = 16,000,460,839 bp (28.65%) number of G's = 11,942,273,132 bp (21.39%) number of N's = 4,199,393 bp (0.01%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 495,315,073 number of insertions = 9,717,076 mapped reads with insertion percentage = 2.28% number of deletions = 26,635,925 mapped reads with deletion percentage = 6.33% homopolymer indels = 44.6% >>>>>>> Coverage mean coverageData = 18.0538X std coverageData = 191.0049X There is a 91.62% of reference with a coverageData >= 1X There is a 91.49% of reference with a coverageData >= 2X There is a 91.32% of reference with a coverageData >= 3X There is a 91.06% of reference with a coverageData >= 4X There is a 90.63% of reference with a coverageData >= 5X There is a 89.94% of reference with a coverageData >= 6X There is a 88.92% of reference with a coverageData >= 7X There is a 87.48% of reference with a coverageData >= 8X There is a 85.55% of reference with a coverageData >= 9X There is a 83.08% of reference with a coverageData >= 10X There is a 80.08% of reference with a coverageData >= 11X There is a 76.53% of reference with a coverageData >= 12X There is a 72.5% of reference with a coverageData >= 13X There is a 68.06% of reference with a coverageData >= 14X There is a 63.3% of reference with a coverageData >= 15X There is a 58.32% of reference with a coverageData >= 16X There is a 53.23% of reference with a coverageData >= 17X There is a 48.14% of reference with a coverageData >= 18X There is a 43.14% of reference with a coverageData >= 19X There is a 38.32% of reference with a coverageData >= 20X There is a 33.75% of reference with a coverageData >= 21X There is a 29.49% of reference with a coverageData >= 22X There is a 25.56% of reference with a coverageData >= 23X There is a 21.99% of reference with a coverageData >= 24X There is a 18.79% of reference with a coverageData >= 25X There is a 15.94% of reference with a coverageData >= 26X There is a 13.45% of reference with a coverageData >= 27X There is a 11.29% of reference with a coverageData >= 28X There is a 9.42% of reference with a coverageData >= 29X There is a 7.83% of reference with a coverageData >= 30X There is a 6.49% of reference with a coverageData >= 31X There is a 5.36% of reference with a coverageData >= 32X There is a 4.42% of reference with a coverageData >= 33X There is a 3.64% of reference with a coverageData >= 34X There is a 3% of reference with a coverageData >= 35X There is a 2.47% of reference with a coverageData >= 36X There is a 2.04% of reference with a coverageData >= 37X There is a 1.69% of reference with a coverageData >= 38X There is a 1.41% of reference with a coverageData >= 39X There is a 1.18% of reference with a coverageData >= 40X There is a 1% of reference with a coverageData >= 41X There is a 0.85% of reference with a coverageData >= 42X There is a 0.74% of reference with a coverageData >= 43X There is a 0.64% of reference with a coverageData >= 44X There is a 0.56% of reference with a coverageData >= 45X There is a 0.5% of reference with a coverageData >= 46X There is a 0.45% of reference with a coverageData >= 47X There is a 0.41% of reference with a coverageData >= 48X There is a 0.38% of reference with a coverageData >= 49X There is a 0.35% of reference with a coverageData >= 50X There is a 0.33% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4543543277 18.22881427043666 436.36663445688583 chr2 243199373 4791666675 19.702627584488056 151.43436530122113 chr3 198022430 3672229991 18.54451534101465 20.417751306286373 chr4 191154276 3639025999 19.037115335050103 150.97022587530273 chr5 180915260 3360243192 18.57357523074615 14.866258311515416 chr6 171115067 3205653019 18.73390271939057 74.84502267255354 chr7 159138663 3015678859 18.950007510117135 155.9403415375311 chr8 146364022 2803973114 19.15752980606122 277.4157859670801 chr9 141213431 2397948267 16.981021210369146 197.6758146893063 chr10 135534747 2906325890 21.443400709635 406.2972093134715 chr11 135006516 2533500459 18.765764305776173 70.95801920734282 chr12 133851895 2467370241 18.433584679544506 12.56665674994976 chr13 115169878 1741041039 15.117156232465575 11.246154058199615 chr14 107349540 1660953655 15.472387259414432 16.53131940243127 chr15 102531392 1549270107 15.110202609947985 11.120945079881992 chr16 90354753 1682439083 18.62037166987773 83.77244906211418 chr17 81195210 1565692311 19.28306252302322 89.99313505844307 chr18 78077248 1508690842 19.323053522583173 192.53054137476875 chr19 59128983 1148007999 19.41531784843991 242.04198378915962 chr20 63025520 1169006256 18.548141387806083 42.65865905948156 chr21 48129895 764229793 15.878484526093398 68.7773060210565 chr22 51304566 685884865 13.368885432146527 17.128079178050285 chrMT 16571 103448562 6242.7470882867665 998.4811207777934 chrX 155270560 2790344489 17.97085351530902 38.89449139026345 chrY 59373566 183014333 3.0824211063893316 172.14207928561154