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
A2 F13 I0 R1 203 85.6 3649704 98.8% 3605907 146.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 1,842,800 T→G 25.1% Q665P (CAG→CCG)  gacS ← sensor protein GacS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC1,842,8000TG25.1% 52.7 / 3.5 35Q665P (CAG→CCG) gacSsensor protein GacS
Reads supporting (aligned to +/- strand):  ref base T (4/21);  new base G (5/4);  total (10/25)
Fisher's exact test for biased strand distribution p-value = 3.43e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGAACAATTCTTCCTGCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGCTCCCCTCGGCCAGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGACAGCAACTGGCCATGGCCGTTGGGCAGGTACGGGTGGTACAGCGCCTGCTCGGT  >  NC_002947_CJ‑RC/1842657‑1842948
                                                                                                                                                |                                                                                                                                                    
cGAACAATTCTTCCTGCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTGGC‑gggggg                                                                                                                                                 >  1:334995/1‑146 (MQ=255)
 gAACAATTCTTCCTGCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTGGC‑gggggcg                                                                                                                                                >  5:364096/1‑145 (MQ=255)
   aCAATTCTTCCTGCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTg                                                                                                                                              <  1:349099/149‑1 (MQ=255)
     aaTTCTTCCTGCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTTGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTggg                                                                                                                                            <  1:107540/149‑1 (MQ=255)
     aaTTCTTCCTGCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTggg                                                                                                                                            <  3:433074/149‑1 (MQ=255)
     aaTTCTTCCTGCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTggg                                                                                                                                            <  6:231420/149‑1 (MQ=255)
        tcttcCTGCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGtt                                                                                                                                         >  2:129135/1‑149 (MQ=255)
             cTGCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGTGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGCTc                                                                                                                                     <  8:433239/148‑1 (MQ=255)
             cTGCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGCTc                                                                                                                                     <  6:244948/148‑1 (MQ=255)
              tGCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTGGC‑GGGGCGGTGGGGtgtgggga                                                                                                                                   >  1:143559/1‑142 (MQ=255)
              tGCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑AGGGCGGTGGGGGTggtgcc                                                                                                                                   >  2:114315/1‑144 (MQ=255)
               gCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑GGGGCGGTGGGGGTggtacc                                                                                                                                   >  4:121085/1‑143 (MQ=255)
                cACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGCTcccc                                                                                                                                  <  2:208383/148‑1 (MQ=255)
                cACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGCTccc                                                                                                                                   <  7:235715/147‑1 (MQ=255)
                  cGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGCTCCCCTCg                                                                                                                               <  1:129135/149‑1 (MQ=255)
                            cgccgcATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑GGGGCGGTGGGGGTGCGGCCCGCGGGCACCgggc                                                                                                                     >  2:325055/1‑147 (MQ=255)
                              ccgcATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGCTCCCCTCGGCCa                                                                                                                           >  7:372926/1‑141 (MQ=255)
                              ccgcATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGCTCCCCTCGGCCa                                                                                                                           <  8:372926/141‑1 (MQ=255)
                                     aCCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTGGCGGGGCCGTTGGGGTTGTACCCACCGGCC‑GCGGGCGGCGCgggt                                                                                                            >  7:2934/1‑147 (MQ=255)
                                         ttgttgACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGCTCCCCTCGGCCAGCGGACGGCGAGGTTGCAc                                                                                                        <  6:425569/149‑1 (MQ=255)
                                          tgttgCCGGACATTACCTCGCCACCCTGGTCTTCGCGCTGGGTTTTTCCCAGCCGCTGGTGGGCGGCATTGTCGTCGACGCAGATTATTTTCGGTCGGCGC‑TGGCCGTTGGGGTTGCTCCCCTCGCCCAGGGGACGGCGAGGTTGCAc                                                                                                        <  4:399394/148‑1 (MQ=255)
                                             tcaCGGCAAGTACCTCGGCACCCAGGTTTTCTAGCTGGGTTTTAACCAGCAGCTGGTTGGCGGATTTGTCGTCGACGAATTTTTTTTTCGGTCGGCGG‑TGGCGGTTGGGGTTGCCCCCCTCGGCAAGCGGACGGCGAGGTTGCACCAg                                                                                                     <  4:60685/146‑1 (MQ=255)
                                              gACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGGTCCCCGCGGCCAGCGGGCGGCGAGGTTGGACCAGcg                                                                                                   >  2:298313/1‑148 (MQ=255)
                                                              gCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGCGGGGCGGGGGGGGTTGGGCCCGCCGGCC‑CCGGGCGGCGGGGTTGGGCCACCGCCACCCACACGcgccg                                                                                   >  1:17809/1‑149 (MQ=255)
                                                                           cGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGCTCCCCTCGGCCAGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCgg                                                                         <  2:102034/146‑1 (MQ=255)
                                                                                     ttttACCAGCAGCTGGTTGGCGGCATTGTGGTCGAGGCTGTTTTTTTTCGGGCGTGGG‑TGGCCGTTGGGGTTGCGCCCCTCGGCCTGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGc                                                             <  6:364096/148‑1 (MQ=255)
                                                                                          cctgcagctgGTGGGGGGCTTTGTGGTCGCCGATGTGTATTTTGGGGCGGCGG‑GGGCGGTGGGGGTTGCTCCCCTGGGCCCGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGAc                                                       <  8:264615/146‑1 (MQ=255)
                                                                                          ccAGCCGCCGGTGGGCGGAATTGGCGTCGCCGCATAGTATTTGCGGCCGTCGG‑GGGCGGTGGGGGTTGCCCCCCGGGCCCAGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGAc                                                       <  7:78622/149‑1 (MQ=255)
                                                                                          ccAGCAGCCGGTGGGCGCCTTGGGCGTCCACCCAGAGTATTTGCGGTCGGCGC‑TGGCGGTGGGGGTGGCCCCCCGCGCCCCGCGCACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGAc                                                       <  7:102665/149‑1 (MQ=255)
                                                                                             gctgcagGTTGGCGGCTTTGTGGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGCTCCCCTCGGCCTGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGACAGc                                                    <  6:208968/146‑1 (MQ=255)
                                                                                                  ttgTTGGGGGAATTGTGGTCTCCCCATTGTTTTTTCGGGCGTCGG‑TGGCGGTTGGGGTTGCTCCCCTCGGCATGGGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGACAGCAACTg                                               <  2:91494/147‑1 (MQ=255)
                                                                                                    gTTGGGGGCATTGTGGGGGACGCTGATTTTTTTGGGTCGGCGG‑TGGCGGTTGGGGTGGCGCCCGTCGGCCAGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGACAGCAACTg                                               <  5:231735/147‑1 (MQ=255)
                                                                                                    gTTGGCGGCATTGTCGGCGACGCAGATTATTTTCGGTCGTCGC‑TGGCGGTTGGGTTTGCTCCCCTCGGCCAGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGACAGCAACTgg                                              <  8:278697/148‑1 (MQ=255)
                                                                                                        gcggcATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGCTCCCCTCGGCCAGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGACAGCAACTGGCCATg                                         <  1:298313/149‑1 (MQ=255)
                                                                                                                 gcgtcgACGCAGAGTATTTGCGGTCGGCGC‑GGGCGGTGGGGGTGCCCCCCCTCGGCCAGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGACAGCAACTGGCCATGGCCGTTggg                                <  3:121085/148‑1 (MQ=255)
                                                                                                                                   tgcGGGCGTCGG‑GGGCGGTGGGGGTGGCGCCCCGCGGCCCGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGACAGCAACTGGCCATGGCCGTTGGGCAGGTACGGGTGGTACa               <  1:114315/146‑1 (MQ=255)
                                                                                                                                            cgC‑TGGCCGTTGGGGTTGCTCCCCTCGGCCAGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGACAGCAACTGGCCATGGCCGTGGGGCAGGTACGGGTGGTACCGCGCCTGCTc     >  5:290195/1‑149 (MQ=255)
                                                                                                                                                tGGCCGTTGGGGTTGCTCCCCTCGGCCAGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGACAGCAACTGGCCATGGCCGTTGGGCAGGTACGGGTGGTACAGCGCCTGCTCggt  >  1:352292/1‑149 (MQ=255)
                                                                                                                                                |                                                                                                                                                    
CGAACAATTCTTCCTGCACGGCCTGTACCGCCGCATAACCATTGTTGACGGCCAGTACCTCGGCACCCAGGTCTTCGAGCAGGGTTTTTACCAGCAGCAGGTTGGCGGCATTGTCGTCGACGCAGAGTATTTTCGGTCGTCGC‑TGGCCGTTGGGGTTGCTCCCCTCGGCCAGCGGACGGCGAGGTTGCACCAGCTCCAGCAAGAGGCGCCGCAGCTTGCGGGTGCAGGTCGGCTTGGACAGCAACTGGCCATGGCCGTTGGGCAGGTACGGGTGGTACAGCGCCTGCTCGGT  >  NC_002947_CJ‑RC/1842657‑1842948

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