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
A12 F59 I0 R4 226 76.6 2995274 95.4% 2857491 127.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 1,026,641 C→A 26.6% S43Y (TCT→TAT)  U712_05035 → Uncharacterized protein yhaP

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068811,026,6410CA26.6% 57.0 / 2.1 44S43Y (TCT→TAT) U712_05035Uncharacterized protein yhaP
Reads supporting (aligned to +/- strand):  ref base C (11/17);  new base A (10/2);  total (25/19)
Fisher's exact test for biased strand distribution p-value = 1.58e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTCTATGAATAAATTTTGGATCATGCTTTCTCATACATACAAAAATAAGATTATGGCAAAATCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGAAAGCGGTGGATACAGACGGCGATCTTGATGTGAAGCTGTCGAAGCAATCG  >  CP006881/1026509‑1026777
                                                                                                                                    |                                                                                                                                        
cGTCTATGAATAAATTTTGGATCATGCGTTCACATACATACAAAAATAAGATTATGGCAAAATCCTTTTTTATTTCGCCTGTAATCACGGTGCTGCGTGTTTTAGTTGTAACGAATCTGGAGTCGATGCTTTCtttttt                                                                                                                                    >  8:83477/1‑139 (MQ=255)
                                  tacatacaAAAATAAGATTATGGCAAAATCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGAGGTTTTCTTTGTTTGTAGGTGGCGATGCGAAATAAAAAATAGCCgtt                                                                                                  >  2:152010/1‑139 (MQ=255)
                                    catacaAAAATAAGATTATGGCAAAATCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGAGGAAATATTTGTTTGAAGTGGACCATAGGAAAGAAAAAATAGCCggtgt                                                                                                >  1:90122/1‑139 (MQ=255)
                                       acaAAAATAAGATTATGGCAAAATCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTCTTTTGTTCAAGGTGACGATGAGAAATAAAAAATAGCCGGTGTtga                                                                                             >  5:343597/1‑139 (MQ=255)
                                         aaaaaTAAGATTATGGCAAAATCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATGAATTATTTTTTTGAAAGGGGAGAAGCGAAAGAAAAAAAAGCCGGTTTtgatg                                                                                           >  6:208179/1‑139 (MQ=255)
                                         aaaaaTAAGATTATGGCAAAATCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATGGGAAAGAAAAAAACGCCGTTGTtgat                                                                                            >  1:259565/1‑138 (MQ=255)
                                         aaaaaTAAGATTATGGCAAAATCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGAGCATTTATTTTTTTCAAGGTGACGATGCGAAAGAAAAAAACGCCGTTGTtgatt                                                                                           >  1:251119/1‑138 (MQ=255)
                                           aaaTAAGATTATGGCAAAATCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTGTTTGTTTGAAGGTGACGATGCGAAATAAAAAATCGCCgttgtttgtga                                                                                          >  2:66175/1‑133 (MQ=255)
                                           aaaTAAGATTATGGCAAAATCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGAGGATTTATTTTTTTTAATGTGAAGATGCGAAAGAAAAAATCGCCGTTGGtgttga                                                                                          >  2:346748/1‑138 (MQ=255)
                                                 gATTATGGCAAAATCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGaaacaaac                                                                                   <  2:208120/139‑1 (MQ=255)
                                                      tGGCAAAATCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAAtt                                                                              <  1:346748/139‑1 (MQ=255)
                                                      tGGCAAAATCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAAtt                                                                              <  1:66175/139‑1 (MQ=255)
                                                            aaTCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTCTTTGTTTGAAGGTGACGATGGGAAAGAAAAAATAGCCCTTGTTGATGAAACAAACGAATTatatac                                                                        >  3:63284/1‑137 (MQ=255)
                                                                        tttCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATGATTTGTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATAGCCGTTGTTGATGAAACAAACGAATTATATGCGGTTTTTTCt                                                              >  2:25599/1‑137 (MQ=255)
                                                                          tCGTCTGGCATCACGGTGCTGCCTGTTTTAGTTGTAACGAACCTGGAGTCGAGCATTTCTTTGTTTCAAGGTGACGATGCGAAAGAAAAACTCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAag                                                           <  7:316269/138‑1 (MQ=255)
                                                                          tCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAag                                                           <  4:354246/138‑1 (MQ=255)
                                                                          tCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAag                                                           <  7:83477/138‑1 (MQ=255)
                                                                          tCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGAGCAATTCTATTTTTCAAGGGGACGCTGCGAAAGAAAAAATAGCCCTTGTTGATGCAAAAAACCAAATATATACCTTTTTTtata                                                             >  5:77039/1‑136 (MQ=255)
                                                                          tCGACTGTCATCACGGGGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAag                                                           <  5:208179/138‑1 (MQ=255)
                                                                                gTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTATTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTATAATCAGCTg                                                     >  8:255662/1‑138 (MQ=255)
                                                                                gTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGAGGAATTGTTTGTTTACAGGTTACCCTGCGAAAGAAAAAATAGCCCGTTTTGATGTAACAAAACAATTATTTACGGTTTTTTATAagccgcag                                                     >  2:302382/1‑136 (MQ=255)
                                                                                   atcaTGGTGTTGTTTGTTTTTTTTTTAACGATTGTGTTTTGTATATTTTATTTTTTTAAATGTGACGAGGGGAATTAAAAAATCGCCTTTGTTGATGAAACAAACTAATTATATCCGGTTTTTTCTAAGCAGCTGaaa                                                  <  2:213914/138‑1 (MQ=255)
                                                                                   atcaGGGTGCTGCTTGTTTTTGTTGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATTCGAAATAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGaaa                                                  <  6:118203/138‑1 (MQ=255)
                                                                                   atcaCGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGaaa                                                  <  7:155024/138‑1 (MQ=255)
                                                                                    gcaCGGGGGTGCTTGGTTTCGTTGTCACGACTCTGGCGGCGAGCATTTCTTTGTTTCAAGGTGACGAGGCGAAACAAAAACTCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGAAAGc                                                <  6:23478/138‑1 (MQ=255)
                                                                                     caCGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGAAAGCg                                               <  2:338927/139‑1 (MQ=255)
                                                                                           gctgctTGTTTTAGTTGTAACGAATCTGGAGTCGATGATTTATTTGTTTAAATGTGACGATGCGAAATAAAAAATCCCCCGTGTTGATGAAAAAAAACAAATATATACGGTTTTTTTTAAGCAGCTGAAAACGGTGGa                                          >  5:118203/1‑138 (MQ=255)
                                                                                             tgctTGTTTTAGTTGTAACGAATCTGGAGTCGAGGATTTTGTTTTTTAAAGGTGAGGCTGGGAAAAAAAAAAAAGCCCGTGTTGTTTTTAAAAAACATATATATTCGGTTTTTTGTTAGACACAGAAAGAGGTGGATa                                        >  2:345172/1‑138 (MQ=255)
                                                                                                    tttAGTTGTAACGAATCTGGAGTCGATCATTTATTTGTTTCAAGGTGACGATGCGAAAGAAAAAATAGCCGTTGTTGATGAAACAAAAGAATTATATACGGTTTTTTCTAAGCAGCAGAAAGCGGTGGATACAGACGGc                                >  6:352442/1‑139 (MQ=255)
                                                                                                    tttAGTTGAAACGAATCTGGAGTCGATAATTTCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGAAAGCGGTGGATACAGACgg                                 <  4:63284/138‑1 (MQ=255)
                                                                                                         ttGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATGCGAAATAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGAAAGCGGTGGATACAGACGGCGATCt                           >  3:93399/1‑139 (MQ=255)
                                                                                                         ttGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGAAAGCGGTGGATACAGACGGCGATCt                           <  6:91739/139‑1 (MQ=255)
                                                                                                            tAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGGCGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAAAAAACGAAATTTATACGGTTTTTTCTAAGCAGCTGAAAGCGGTGGATACAGACGGCGATATTGa                        >  1:51734/1‑139 (MQ=255)
                                                                                                              aCGAATCTGGAGTCGATCATTTATTTGTTTGAAGGTGCCGATGCGAAAGAAAAAATACCCGTTGTTGATGAAACAAACCAATTATTTACCGTTTTTTCTAAGCACCTGAAAGCCGTGGATACAGACGGCGATATTGAtt                      >  6:224483/1‑138 (MQ=255)
                                                                                                                        aGTCTATCATTTATTTGTTTCATGGTGAGCATGCTAACCAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGAAAGCGGTGGATACAGACGGCGATCTTGATGTGAAGCTGTc            <  6:30196/139‑1 (MQ=255)
                                                                                                                            gagccgttCGTTGTTTCCAGGTGCCGATGCGAAAGAAAAAATCGCCGGTGGTGATGAAACCAACGAATTATATCCGGGTTTTTATTAGCAGCTGCAAGCGGGGGATACAGACGGCGATCTTGATGTGAAGCTGTCGAAg        >  7:15751/7‑139 (MQ=255)
                                                                                                                            gATCATTTCTTTGTTTCAAGGTGACGATGCGAACTAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGAAAGCGGTGGATACAGACGGCGATCTTGATGTGAAGCTGTCGAAg        <  4:258180/139‑1 (MQ=255)
                                                                                                                            gATCATTTCTTTGTTTCAAGGTGACGATGCGAAATAAAAAATAGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGAAAGCGGTGGATACAGACGGCGATCTTGATGTGAAGCTGTCGAAg        >  7:154087/1‑139 (MQ=255)
                                                                                                                            gATCATTTATTTGTTTCAAGGTGACGATTCGAAACAAAAAATCGCCGTTGTTGATGAAACAAAAGAATTATATACGGTTTTTTCTAAGCAGCTGAAAGCGGTGGATACAGACGGCGATCTTGATGTGAAGCTGTCGAAg        >  3:120933/1‑139 (MQ=255)
                                                                                                                             aTCATTTATTTGTTTCAAAGTGACCATGCGAAATAAAAAATCCCCGTTGTTGATGAAACAAACGAATTATATACGGTTTTTTCTAATCAGCTGAAAGCGGTTGATAAAGACGGCGAACTTGATGTGAAGATGTCGaat        >  8:258925/1‑137 (MQ=255)
                                                                                                                                aTTTCTTTGTTTCCAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGAAAGCGGTGGATACAGACGGCGATCTTGATGTGAAGCTGTCGAAGCAAt    <  1:239459/139‑1 (MQ=255)
                                                                                                                                  ttCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGaaacaa                                                                                     >  1:51351/1‑56 (MQ=255)
                                                                                                                                  ttCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGaaacaa                                                                                     <  2:51351/56‑1 (MQ=255)
                                                                                                                                   tCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGAAAGCGGTGGATACAGACGGCGATCTTGATGTGAAGCTGTCGAAGCAATCg  <  2:251119/138‑1 (MQ=255)
                                                                                                                                    cTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGAAAGCGGTGGATACAGACGGCGATCTTGATGTGAAGCTGTCGAAGCAATCg  >  5:146362/1‑137 (MQ=255)
                                                                                                                                    |                                                                                                                                        
CGTCTATGAATAAATTTTGGATCATGCTTTCTCATACATACAAAAATAAGATTATGGCAAAATCCTTTATTATTTCGACTGTCATCACGGTGCTGCTTGTTTTAGTTGTAACGAATCTGGAGTCGATCATTTCTTTGTTTCAAGGTGACGATGCGAAAGAAAAAATCGCCGTTGTTGATGAAACAAACGAATTATATCCGGTTTTTTCTAAGCAGCTGAAAGCGGTGGATACAGACGGCGATCTTGATGTGAAGCTGTCGAAGCAATCG  >  CP006881/1026509‑1026777

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A