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
A23 F79 I1 R1 20 28.5 998386 94.1% 939481 141.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 4,111,596 G→A L179L (CTG→TTG)  yiiQ ← DUF1454 family putative periplasmic protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA4,111,5960GA96.0% 73.1 / NA 25L179L (CTG→TTG) yiiQDUF1454 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (15/9);  minor base T (0/1);  total (15/10)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

AAAGGAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGAT  >  NC_000913_3_pae_tpiA/4111451‑4111740
                                                                                                                                                 |                                                                                                                                                
aaaGGAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTAAGATAGCGCCAGCTTAATCGGTTCAACAGCCAAGCTCAAccc                                                                                                                                               >  2:283954/1‑149 (MQ=255)
    gAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCttt                                                                                                                                           <  2:1888/149‑1 (MQ=255)
           gccgccCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGt                                                                                                                                    >  2:312201/1‑149 (MQ=255)
                 ccGTAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCcg                                                                                                                              <  2:369483/149‑1 (MQ=255)
                 ccGCAGGGCAGCAGGTCTTTGAAGCAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCcg                                                                                                                              <  2:324921/149‑1 (MQ=255)
                         tagcagGTATGGGAAACAGGAGAGAGATTGAGCGGCACAAAGGGTGTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGacaaca                                                                                                                      <  2:220090/148‑1 (MQ=255)
                                tCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCa                                                                                                               >  2:31629/1‑149 (MQ=255)
                                   gtgAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTg                                                                                                            <  1:273449/149‑1 (MQ=255)
                                              taGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCTTTGTCCGCGACAACATAACGCAGTGAACCTTCTGtc                                                                                                 >  1:207237/1‑149 (MQ=255)
                                                   aTTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGgt                                                                                            <  1:312201/149‑1 (MQ=255)
                                                             acaAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCTCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACgt                                                                                  >  2:235504/1‑149 (MQ=255)
                                                             acaAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACgt                                                                                  >  1:463034/1‑149 (MQ=255)
                                                               aaaGGCTTTGCTTTTTGTCATTTATTCACACCTTCAAGCGATTCAGATAGCGCCAGCTGAATAGGTTCAACAGCTAGGGTCAACACCTCTTCGCCGTTTGCCGCGACAACCTAACTCAGTGCACCTTCTGTCTCGGTGTAGTAACcttt                                                                                >  2:81611/1‑149 (MQ=255)
                                                                                  aTTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTtagt                                                             >  1:483762/1‑149 (MQ=255)
                                                                                       ttCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCgc                                                        >  1:238530/1‑148 (MQ=255)
                                                                                        tccaaCCTTCAAGCGATTCAGATATCACCAGCTTAATGGGTTCAACAGCTAATGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCATTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGAc                                                       <  2:463034/146‑1 (MQ=255)
                                                                                                   aGCGATTCAGATAGCGCCAGCTTAATCGGTTCGACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGtttttt                                            >  2:109190/1‑149 (MQ=255)
                                                                                                    gtgATTCAGAATGCGCAAGCTTAAGCGGTACAACAGTGAAGGTCATCCTTTTTTCGAAGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTc                                           <  2:48484/147‑1 (MQ=255)
                                                                                                     cGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCt                                          <  1:161748/149‑1 (MQ=255)
                                                                                                             aTAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTTTGGCttttt                                  >  1:114077/1‑147 (MQ=255)
                                                                                                                  gcCAGCTTAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGtttt                             <  1:77910/149‑1 (MQ=255)
                                                                                                                         tAATCGGTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCAtt                      >  1:337673/1‑149 (MQ=255)
                                                                                                                               gTTCAACAGCGAAGGTCAACCCCTTTTCGCCGTTCTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGATTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATggg                >  2:396136/1‑149 (MQ=255)
                                                                                                                                ttCAACAGCGAAGGTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATgggg               >  2:120764/1‑149 (MQ=255)
                                                                                                                                             gTCAACCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGAt  >  2:261260/1‑149 (MQ=255)
                                                                                                                                                 |                                                                                                                                                
AAAGGAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAACAGTATAGAGATTCATCGGCACAAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTTCGCCGTTGTCCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTTCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGAT  >  NC_000913_3_pae_tpiA/4111451‑4111740

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A