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
A1 F14 I0 R1 248 61.6 2601574 98.7% 2567753 146.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 5,123,536 A→C 23.2% L306R (CTG→CGG)  PP_4508 ← AraC family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC5,123,5360AC23.2% 52.6 / 2.7 42L306R (CTG→CGG) PP_4508AraC family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (17/12);  new base C (3/6);  total (20/22)
Fisher's exact test for biased strand distribution p-value = 2.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTCGGGCAACTACGCCACGCTGCCTGACGCGGCCAAATGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTCATGCCCGGCTGGGCCAGGTATTGTTCGGCCAGTTCGC  >  NC_002947_CJ‑RC/5123391‑5123680
                                                                                                                                                 |                                                                                                                                                
cGTCGGGCAACTACGCCACGCTGCCTGACGCGGCCAAATGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAggc                                                                                                                                               <  2:96516/149‑1 (MQ=255)
    gggCAACTACGCCACGCTGCCTGACGCGGCCAAATGGATTCTGGCGGCCGGCATGCTGTTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAggcgggc                                                                                                                                           >  7:224587/1‑149 (MQ=255)
     ggCAACTACGCCACGCTGCCTGACGCGGCCAAATGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAggcgggcg                                                                                                                                          >  1:31610/1‑149 (MQ=255)
      gCAACTACGCCACGCTGCCTGACGCGGCCAAATGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGgcgc                                                                                                                                         >  7:50681/1‑149 (MQ=255)
          cTACGCCACGCTGCCTGACGCGGCCAAATGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCGCCTGGGCGCggaa                                                                                                                                     <  5:209952/149‑3 (MQ=255)
          cTACGCCACGCTGCCTGACGCGGCCAAATGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCGCCTGGGCGCggaa                                                                                                                                     <  5:100768/149‑3 (MQ=255)
          cTACGCCACGCTGCCTGACGCGGCCAAATGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTa                                                                                                                                     >  2:28256/1‑149 (MQ=255)
           tACGCCACGCTGCCTGACGCGGCCAAATGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTAc                                                                                                                                    >  7:99432/1‑149 (MQ=255)
                cACGCTGCCTGACGCGGCCAAATGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCAGCGCCCACGCGGGCGCGGGAcaag                                                                                                                                 >  5:244078/1‑144 (MQ=255)
                        cTGACGCGGCCAAATGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTTCTCGCTGGGCGTgg                                                                                                                       >  1:207916/1‑149 (MQ=255)
                            cgcgGCAAAATGTATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGTAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATc                                                                                                                   <  8:50681/149‑1 (MQ=255)
                            ccccgCCAAATGGAATCTGCCGGCCGGCTTGCGGCTGGGTCGCCTGCAAATCACCCCGGTTGTGGTGGTCTCCACCCCGCCGCTCTGCCGCCACGCCGCACTTCCCCTACCGCCCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATc                                                                                                                   <  6:296785/145‑1 (MQ=255)
                             gcgGCCAAATGGATTTTGGCGGCGGGCATGCTGCTGGGTCGCTTGTAAATCATAACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGGGTCACTGAGCACTTCGCCTTCCGCGCCCTGGCGGGGGCGGTACTCGCTGGGCGTGGCATCg                                                                                                                  <  4:261024/149‑1 (MQ=255)
                              cgGCCAAATGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCg                                                                                                                  >  2:260377/1‑148 (MQ=255)
                               ggCCAAATGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGCTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCCGGCCCGCCCGCTACGCCCTCGGCCTGGCCTCgca                                                                                                                >  8:292068/1‑147 (MQ=255)
                                   aaaTGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCCGGCCGGCGCGGGACTCCCTGGGCGTGGGATCGCACCAg                                                                                                            >  3:48895/1‑149 (MQ=255)
                                       ggATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGGATCGAACCAGCGAc                                                                                                        >  3:271540/1‑149 (MQ=255)
                                                       caggtggctgGGCCGCCTGTAAATCACCCCGGTGTTGGTGTTGTGCTGGCCGGGGTTCTGGCGTCCCTGACCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGaa                                                                                        <  8:323651/143‑1 (MQ=255)
                                                            tgctgGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGc                                                                                   >  3:141564/1‑149 (MQ=255)
                                                                 ggTCGCCTGGAAATCATCACGGGGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTggg                                                                               <  2:195589/148‑1 (MQ=255)
                                                                   tCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCCGGCGGGCGGGGTTCTCGCGGGGCGTGGGATGGAACCAGCGGCGGCACGCCCGATATAAGTTTCTGGGGTc                                                                            >  2:115549/1‑149 (MQ=255)
                                                                      ccTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTGCGGGGGTCACTGAGCACTTCGCCTTCCGCGCCCAGGGGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGc                                                                         <  8:99432/149‑1 (MQ=255)
                                                                          taaaTAATCAGGGTTTGGGTGTTGTGCATGCCGGGGTTCGGGCGCCACTGACCACTTCGCCTTCCGCCCCCCGGGGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAg                                                                     <  5:112048/148‑1 (MQ=255)
                                                                             atcatcACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGcc                                                                   >  5:225236/1‑148 (MQ=255)
                                                                                    cGGTGTTGGTGTTGTGCAGGCGGGCGTTGTGGGTCCATTGCCAACTTCTCATTCCGGCCCCGGGGGGTGGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACTCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGt                                                           <  6:244078/149‑1 (MQ=255)
                                                                                    cGGTGTGCGTGTTGTGCATGCCGGCGTTCTGGCGGCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGt                                                           <  2:207916/149‑1 (MQ=255)
                                                                                            gtgttgTGCATGCGGGGGGTGTGGCGTCACTGCGCCCTTCGCCTTCGGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGtt                                                   <  2:98167/149‑1 (MQ=255)
                                                                                                 gtgCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCCGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCa                                               <  5:151189/148‑1 (MQ=255)
                                                                                                    cttGCGGGCGTTGTGGCGTCACTTAGCACTTCGCCTTCGGCGCCCCGGGGGGGGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCaa                                           <  6:170861/147‑1 (MQ=255)
                                                                                                       gcgggCGTTGTGGCGTCACTGACCACTGCCCCTCCCGCGCCCCGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAgg                                         <  4:141564/145‑1 (MQ=255)
                                                                                                         cGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCCAAAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTCa                                      >  6:234057/1‑149 (MQ=255)
                                                                                                                 tGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTCATGCCCGGc                              >  7:11949/1‑149 (MQ=255)
                                                                                                                   gCGTCACTGACCACTGCCCCTCCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTCATGCCCGGCTg                            <  8:224587/149‑1 (MQ=255)
                                                                                                                            cgCACTGCGCCTCCCGCCCCCCGGGGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTCATGCCCGGCTGGGCCAGGTa                   <  3:240419/148‑1 (MQ=255)
                                                                                                                                cTTCGCCTTCCGCGCCCAGGGGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTCATGCCCGGCTGGGCCAGGTATTGt               <  1:260377/149‑1 (MQ=255)
                                                                                                                                cTTCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGGATCGAACCAGCGACGGAACGCCCGATAGAAGTTGGTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTGATGCCCGGCTGGGCCAGGTATTGt               >  8:305509/1‑149 (MQ=255)
                                                                                                                                 ttCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGACCCAGCGCCGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTCATGCCCGGCTGGGCCAGGTATTGtt              >  8:188584/1‑149 (MQ=255)
                                                                                                                                   cGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTCATGCCCGGCTGGGCCAGGTATTGtt              <  6:154891/147‑1 (MQ=255)
                                                                                                                                   cGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTCATGCCCGGCTGGGCCAGGTATTGTTCg            >  8:161019/1‑149 (MQ=255)
                                                                                                                                     ccTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTCATGCCCGGCTGGGCCAGGTATTGTTCGGc          <  8:282095/149‑1 (MQ=255)
                                                                                                                                      cTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTCATGCCCGGCTGGGCCAGGTATTGTTCGGc          >  5:5258/1‑148 (MQ=255)
                                                                                                                                             gcCCCGGGGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTCATGCCCGGCTGGGCCAGGTATTGTTCGGCCAGTTcgc  <  5:241042/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                
CGTCGGGCAACTACGCCACGCTGCCTGACGCGGCCAAATGGATTCTGGCGGCCGGCATGCTGCTGGGTCGCCTGGAAATCATCACGGTGTTGGTGTTGTGCATGCCGGCGTTCTGGCGTCACTGAGCACTTCGCCTTCCGCGCCCAGGCGGGCGCGGTACTCGCTGGGCGTGGCATCGAACCAGCGACGGAACGCCCGATAGAAGTTGCTGGGGTCGGCAAAGCCCAGCAGGTAGGCGGTTTCCAGCAAGGTCATGCCCGGCTGGGCCAGGTATTGTTCGGCCAGTTCGC  >  NC_002947_CJ‑RC/5123391‑5123680

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