Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A3 F14 I0 R1 206 76.7 3255580 98.8% 3216513 146.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 2,294,024 C→G 22.5% R7G (CGG→GGG)  PP_2020 → lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC2,294,0240CG22.5% 59.3 / 3.8 34R7G (CGG→GGG) PP_2020lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (17/9);  new base G (4/4);  total (21/13)
Fisher's exact test for biased strand distribution p-value = 6.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCTGATGCTGACCTTCATGCTGCTTTGGAACATGTTTGGTGCGCTGTGGCTGCTACCGGCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGCGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTGCACGCCTTCGATTTCACCGTTGATGAAGCCGGCCTCACTGTCGAAT  >  NC_002947_CJ‑RC/2293876‑2294171
                                                                                                                                                       |                                                                                                                                                    
ccTGATGCTGACCTTCATGCTGCTTTGGAACATGTTTGGTGCGCTGTGGCTGCTACCGGCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGc                                                                                                                                                      <  3:146905/149‑1 (MQ=255)
 cTGATGCTGACCTTCATGCTGCTTTGGAACATGTTTGGTGCGCTGTGGCTGCTACCGGCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGCg                                                                                                                                                     <  4:233565/149‑1 (MQ=255)
                 tgctgcTTTGGAACATGTTTGGTGCGCTGTGGCTGCTACCGGCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGCGG‑CCCCCCGGGtataa                                                                                                                                     >  5:80201/1‑147 (MQ=255)
                  gctgctTTGGAACATGTTTGGTGCGCTGTGGCTGCTACCGGCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGCGG‑c                                                                                                                                                  <  4:211576/134‑1 (MQ=255)
                  gctgctTTGGAACATGTTTGGTGCGCTGTGGCTGCTACCGGCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGCGG‑c                                                                                                                                                  >  3:211576/1‑134 (MQ=255)
                   ctgctTTGGAACATGTTTGGTGCGCTGTGGCTGCTACCGGCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGCGG‑CCCCCCGGTTTTACTg                                                                                                                                   >  7:242808/1‑148 (MQ=255)
                      ctTTGGAACATGTTTGGTGCGCTGTGGCTGCTACCGGCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGGCGCCTTTGGGG‑CCCCCCGGTtttatgggcg                                                                                                                                >  3:335220/1‑143 (MQ=255)
                               aTGTTTGGTGCGCTGTGGCTGCTACCGGCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCC‑CATTGCGG‑CCCCCCGGGTTTAATGCCCGCTCAttt                                                                                                                        >  1:83748/1‑147 (MQ=255)
                                              tgGCTGCTACCGGCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CCTTGGGG‑CCCCCCGGGTTTTAAGGCAGCGGATTTGAGATGGGGAgcccga                                                                                                        >  7:6975/1‑146 (MQ=255)
                                                   gctACCGGCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGGCG‑CCTTGGGG‑GCCCCCCGGTATACGTGCAGCTGCATTGAGATGGGGTCGCCGATGTcc                                                                                                   >  5:128071/1‑148 (MQ=255)
                                                         ggCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGCGG‑CCACCCGGTTATAATTGCAGCTCATTTCAGATTGGTACCCCTATGTccccccac                                                                                             >  8:398185/1‑146 (MQ=255)
                                                          gCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGCGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCg                                                                                            >  8:240315/1‑148 (MQ=255)
                                                             ttGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTTCGG‑CCCCCCGGGTTTAATGGCCGCGCATTTAAGATGGGTTCCCCGATGTCCCCCCCCGcga                                                                                         >  7:48913/1‑146 (MQ=255)
                                                                        ccTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTTCGG‑CCCCCCGGTTTTTATGCCAGCTGATTTGAGATGGGTTACCCAATGTCCCCCCAACCTACCCCCCAGCAGt                                                                             >  1:17282/1‑149 (MQ=255)
                                                                         cTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGCGG‑CCCCCCGGGTATACTGCCAGCTCATTTAAGATGGGTACCCCTATGTGCCCCCACCCTACCCCCCAGCAGt                                                                             >  5:101910/1‑148 (MQ=255)
                                                                         cTGATAAAGCCTGCGAAGTTGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGTTTGGC‑GGGGGCCC‑CATTGGGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGt                                                                             <  6:69115/148‑1 (MQ=255)
                                                                           gATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTTCGG‑CCCCCCGGGTTTTCTGCCAGCGCATTTGAGATGGGTTCCCCAATGTACCCCCACGCTACCCCCCGGCAGtgc                                                                           >  6:41703/1‑146 (MQ=255)
                                                                           gATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGCGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTcc                                                                           >  6:90846/1‑148 (MQ=255)
                                                                            aTCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGC‑GGGGGCCG‑CATTGCTG‑CCCCCCGGGTATACAGCCAGCGCATTTCCGAGGGGTTCCCCGATGTGCCCCCTCGCAACCGCCCAGCAGTACt                                                                          >  8:113702/1‑148 (MQ=255)
                                                                                aGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGGCC‑CATTGCGG‑CCCCCCCGTTATTATGGCAGCGAAATTATTAATGGTACACCAATGTGCCCCCAAGCGACCCCCCAGCACTCCTGc                                                                        >  8:273587/1‑146 (MQ=255)
                                                                                     gagaAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGCGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGGGATATggt                                                                >  2:26890/1‑147 (MQ=255)
                                                                                        catgtgggggGCAATGGGGGGGGGGCCTATCTTCCCCATTTTTTTGGG‑GGGGGCCG‑‑ATTGGGGCCCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCt                                                                <  5:41703/143‑1 (MQ=255)
                                                                                            tgggggGCAA‑GGCGGGGGGGCCTACCTTCCCCCTTTTATTGGA‑GGGGGCCG‑CATTCGGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGa                                                           <  6:45813/147‑1 (MQ=255)
                                                                                                       ggaggGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGCGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTg                                                >  2:327830/1‑148 (MQ=255)
                                                                                                          gggtgggtCGATCTTCGCCCATTGATTGGAGGGGGGCCC‑CATTGGGC‑CCCCCCGGTT‑TACAGAGCGCGCCATTAACATAGGTAGCCCAATGTCCCCCCGACCGACCGCCCAGCAGTGCGGCGGTAAAGTTTTTATAGCCGGCCAGcgcc                                            >  2:174463/1‑146 (MQ=255)
                                                                                                          gggtgggtCGATCTTCGCCCATTGATTGGA‑GGGGGCCC‑CAATGCGG‑CCCCCCGGTTATAATGCCCGCTCAGTTAATATTGGTTCCCCAATTTCCCCCCTCGCGACCCCCCCGCAGTCCGGCGGTTTTGTTTTTTTAGACGGCCAGCAcc                                            >  2:331716/1‑148 (MQ=255)
                                                                                                                    aTCTCCCCCCATTGATTGGC‑GGGGCCCG‑CATTGCGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTGCACGCCTTCGAtta                                  <  4:335220/149‑2 (MQ=255)
                                                                                                                         cGCCCTTTGTTTTGT‑GGGGGCCG‑CATTGCGG‑CCCCCCGGGTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTGCACGCCTTCGAt                                    <  6:128071/142‑1 (MQ=255)
                                                                                                                          gCCCATTGTTGGGT‑GGGGGCCG‑CTTTGCGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATTGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTGCACGCCTTCGATTTCACCg                             <  7:113702/148‑1 (MQ=255)
                                                                                                                            ccATTGATTGGA‑GGGGGCCG‑CATTGCGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTGCACGCCTTCGATTTCACCGtt                           <  8:6975/148‑1 (MQ=255)
                                                                                                                             cttttattgGA‑GGGGGCCT‑CATGGGGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTGCACGCCTTCGATTTCACCGTtga                         <  1:600/144‑1 (MQ=255)
                                                                                                                                              ccG‑CATTGCGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTGCACGCCTTCGATTTCACCGTTGATGAAGCCGGCCTCAc          <  8:48913/148‑1 (MQ=255)
                                                                                                                                                  cATTGCGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATTGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTGCACGCCTTCGATTTCACCGTTGATGAAGCCGGCCTCACTGt       <  8:170195/148‑1 (MQ=255)
                                                                                                                                                  cATTGCGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTGCACGCCTTCGATTTCACCGTTGATGAAGCCGGCCTCACTg        <  6:206709/147‑1 (MQ=255)
                                                                                                                                                  cATTGCGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTGCACGCCTTCGATTTCACCGTTGATGAAGCCGGCCTCACTg        >  5:206709/1‑147 (MQ=255)
                                                                                                                                                      gcgc‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTGCACGCCTTCGATTTCACCGTTGATGAAGCCGGCCTCACTGTCGAAt  <  1:214450/149‑1 (MQ=255)
                                                                                                                                                       cGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTGCACGCCTTCGATTTCACCGTTGATGAAGCCGGCCCCACTGTCGaa   <  7:227666/147‑1 (MQ=255)
                                                                                                                                                       |                                                                                                                                                    
CCTGATGCTGACCTTCATGCTGCTTTGGAACATGTTTGGTGCGCTGTGGCTGCTACCGGCATTGGCGCGGTTCCTGATCAAGCCTGAGAAGATGGTGGGCAA‑GGAGGGTGGGTCGATCTTCGCCCATTGATTGGA‑GGGGGCCG‑CATTGCGG‑CCCCCCGGTTATACTGCCAGCTCATTTCAGATGGGTACCCCTATGTCCCCCCTCGCTACCGCCCTGCAGTCCTGCGATATGCTTTTGATCGACGGCCTGCACGCCTTCGATTTCACCGTTGATGAAGCCGGCCTCACTGTCGAAT  >  NC_002947_CJ‑RC/2293876‑2294171

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A