BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505956.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 = 12,434,164 number of mapped reads = 10,123,027 (81.41%) number of supplementary alignments = 415 (0%) number of secondary alignments = 0 number of mapped bases = 475,340,902 bp number of sequenced bases = 475,238,032 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 540,683 duplication rate = 3.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2234 >>>>>>> ACTG content number of A's = 144,489,841 bp (30.4%) number of C's = 93,945,641 bp (19.77%) number of T's = 141,578,836 bp (29.79%) number of G's = 95,222,163 bp (20.04%) number of N's = 1,551 bp (0%) GC percentage = 39.8% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 2,164,959 number of insertions = 20,523 mapped reads with insertion percentage = 0.2% number of deletions = 73,714 mapped reads with deletion percentage = 0.73% homopolymer indels = 48.61% >>>>>>> Coverage mean coverageData = 0.1535X std coverageData = 1.4487X There is a 10.71% of reference with a coverageData >= 1X There is a 2.99% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 50358740 0.20204057987081203 3.3242360810110045 chr2 243199373 30352393 0.12480456929467496 0.8839457887125404 chr3 198022430 31040896 0.1567544444333907 0.5560961783388206 chr4 191154276 21346080 0.11166938269275233 0.44313727320331026 chr5 180915260 28560020 0.15786407404217864 0.5445982919500157 chr6 171115067 35140257 0.20536039061948883 1.1207643866681394 chr7 159138663 34358843 0.21590506261825262 2.7920296098410624 chr8 146364022 30970475 0.2115989611162776 1.9596396196193928 chr9 141213431 13937379 0.09869726201893643 0.7600152498688384 chr10 135534747 15457369 0.11404727822305227 1.4068823485989694 chr11 135006516 25933498 0.19209071360674176 1.240404337285026 chr12 133851895 14108884 0.10540668101859896 0.515716463061198 chr13 115169878 14080379 0.12225747951213424 0.4513878733128399 chr14 107349540 17862591 0.16639653043692595 0.5786147770300186 chr15 102531392 8876966 0.08657803065816175 0.37732103396501476 chr16 90354753 14875006 0.1646289266044477 0.6952949565390651 chr17 81195210 7325757 0.09022400459337442 0.5683636865366327 chr18 78077248 12533842 0.16053129843920727 1.7124253130256466 chr19 59128983 10929793 0.18484662589241557 2.030475416066109 chr20 63025520 11288831 0.17911523776400418 0.5687313036041621 chr21 48129895 7558315 0.15703992290030966 0.5983431874098715 chr22 51304566 3012105 0.05871027151852332 0.3257854390350318 chrMT 16571 31934 1.927101562971456 1.8405341503587955 chrX 155270560 34161052 0.22000984603906884 0.8753956631824539 chrY 59373566 1239497 0.02087624314160278 0.2497777426421219