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 F1 I1 R1 14 24.7 1576304 96.5% 1521133 75.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 2,108,753 C→T G254S (GGC→AGC)  ECB_01996 ← baseplate assembly protein J

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6062,108,7530CT94.7% 51.4 / ‑5.5 19G254S (GGC→AGC) ECB_01996baseplate assembly protein J
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (10/8);  total (10/9)
Fisher's exact test for biased strand distribution p-value = 4.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

AGAAAGACGCCTGCGTGCTGTTAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCCTTCCACATGCAAAGCGGCATAAATGGCAGACAGACGGATGTCGCGCCCCAGCCGGTGCTGTGCCGTGATGT  >  REL606/2108684‑2108824
                                                                     |                                                                       
aGAAAGACGCCTGCGTGCTGTTAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTcccc                                                                   >  1:348755/1‑74 (MQ=255)
  aaaGACGCCTGCGTGCTGTTAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACAt                                                                 >  1:181572/1‑76 (MQ=255)
   aaGACGCCTGCGTGCTGTTAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATg                                                                >  1:308162/1‑76 (MQ=255)
     gACGCCTGCGTGCTGTCAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCa                                                              <  2:512298/76‑1 (MQ=255)
        gCCTGCGTGCTGTTAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACCCGCTGCACGCTTTCCACATGcgca                                                            >  2:673372/1‑72 (MQ=255)
        gCCTGCGTGCTGTTAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCaca                                                            <  1:673372/75‑3 (MQ=255)
         ccTGCGTGCTGTTAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCAAAGc                                                          <  1:555577/76‑1 (MQ=255)
             cGTGCTGTTAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCAAAGCGGCa                                                      >  2:423111/1‑76 (MQ=255)
                   gTTAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCAAAGAGGCATaaaag                                                >  1:98660/1‑74 (MQ=255)
                    ttAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCAAAGCGGCATAAATgg                                               >  2:323363/1‑76 (MQ=255)
                     tAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCAAAGCGGCATAAATGGc                                              <  1:162556/76‑1 (MQ=255)
                     tAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCAAAGCGGCATAAATGGc                                              <  2:385460/76‑1 (MQ=255)
                          aCGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCAAAGCGGCATAAATGGcagaca                                         <  1:427277/76‑1 (MQ=255)
                            gATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCAAAGCGGCCTAAATGGcagacaga                                       >  2:356032/1‑76 (MQ=255)
                            gATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCAAAGCGGCATAAATGGcagacaga                                       <  2:740011/76‑1 (MQ=255)
                                   gCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCAAAGCGGCATAAATGGCAGACAGACGGATGt                                >  2:471431/1‑76 (MQ=255)
                                     cggCGGTGCAGCCAGTTCGGCACGCGGCACGCTTTCCACATGCAAAGCGGCATAAATGGCAGACAGACGGATGTcg                              <  2:215128/74‑1 (MQ=255)
                                      gtcGGTGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCAAAGCGGCATAATTGGCAGACAGACGGATGTcgc                             >  2:656173/3‑76 (MQ=255)
                                           tGCAGCCAGTTCGACACGCTGCACGCTTTCCACATGCAAAGCGGCATAAATGGCAGACAGACGGATGTCGCGcccc                        >  1:406334/1‑76 (MQ=255)
                                                  aGTCCGCCACGCTGCACGCTTTCCACATGCAAAGCGGCATAAATGGCAGACAGACGGATGTCGCGCCCCAGCCGGt                 <  2:70080/76‑1 (MQ=255)
                                                             cTGCCCGCTTCCCACATGCAAAGCGGCATAAATGGCAGACAGCGGGATGCCGCGCCCCAGCCGGTGCTGTGCCGTg      <  1:423111/76‑1 (MQ=255)
                                                               gCACGCTTTCCACATGCAAAGCGGCATAAATAGCAGACAGACGGATGTCGCGCCCCAGCCGGTGCTGTGCCGTGAt    >  2:625489/1‑76 (MQ=255)
                                                                 aCGCCTTCCACATGCAAAGCGGCATAAATGGCAGACAGACGGATGTCGCGCCCCAGCCGGTGCTGTGCCGTGATGt  <  2:495783/76‑1 (MQ=255)
                                                                     |                                                                       
AGAAAGACGCCTGCGTGCTGTTAAGCACGATATCGGCCAGCGGTGCAGCCAGTTCGACACGCTGCACGCCTTCCACATGCAAAGCGGCATAAATGGCAGACAGACGGATGTCGCGCCCCAGCCGGTGCTGTGCCGTGATGT  >  REL606/2108684‑2108824

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A