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
A5 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,604,824 G→A 13.5% S16S (AGC→AGT)  yjjA ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,604,8240GA13.5% 251.3 / 24.5 89S16S (AGC→AGT) yjjAconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (35/42);  new base A (5/7);  total (40/49)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTTCGCTGGCGGCGCTGGAGAGCGCATCTTTCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCAAGGTGGAATTG  >  W3110S.gb/4604756‑4604891
                                                                    |                                                                   
aGTTCGCTGGCGGCGCTGGAGAGCGCATCTTTCCAGGACGCAGCATGCACCCCGGTGGAAATTAATgcgc                                                                    >  1:381067/1‑70 (MQ=255)
aGTTCGCTGGCGGCGCTGGAGAGCGCATCTTTCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCt                                                                   >  1:934447/1‑71 (MQ=255)
aGTTCGCTGGCGGCGCTGGAGAGCGCATCTTTCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCt                                                                   >  1:2487113/1‑71 (MQ=255)
aGTTCGCTGGCGGCGCTGGAGAGCGCATCTTTCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCt                                                                   >  1:2498276/1‑71 (MQ=255)
aGTTCGCTGGCGGCGCTGGAGAGCGCATCTTTCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCt                                                                   >  1:3384439/1‑71 (MQ=255)
aGTTCGCTGGCGGCGCTGGAGAGCGCATCTTTCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCt                                                                   >  1:2733555/1‑71 (MQ=255)
      cTGGCGGCGCTGGAGAGCGCATCTTTCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCTggcggc                                                             <  1:2966709/71‑1 (MQ=255)
       tGGCGGCGCTGGAGAGCGCATCTTTCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCTggcggc                                                             <  1:500497/70‑1 (MQ=255)
           gtcgcTGGAGAGCGCATCTTTCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATgg                                                        <  1:3175610/69‑1 (MQ=255)
                       cgcATCTTTCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCACTGGCGGCAATGGCACAGCACagaa                                            <  1:3611174/71‑1 (MQ=255)
                           tCTTTCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCTggcggc                                                             <  1:2119771/50‑1 (MQ=255)
                             tttCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGtt                                      >  1:1411196/1‑71 (MQ=255)
                             tttCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGtt                                      >  1:4866574/1‑71 (MQ=255)
                               tCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGttt                                     >  1:4875203/1‑70 (MQ=255)
                                ccAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGtt                                      <  1:696371/68‑1 (MQ=255)
                                 cAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCTTGCGGCAATGGCACAGCACAGAAGATGTTTaa                                   <  1:3744001/70‑1 (MQ=255)
                                 cAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTaa                                   <  1:411709/70‑1 (MQ=255)
                                 cAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTaa                                   <  1:2019384/70‑1 (MQ=255)
                                   ggACGCAGCATGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAg                                <  1:2508431/71‑1 (MQ=255)
                                    gACGCAGCATGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGt                               <  1:3282122/71‑1 (MQ=255)
                                    gACGCAGCATGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGt                               >  1:5064728/1‑71 (MQ=255)
                                    gACGCAGCATGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGt                               >  1:3393373/1‑71 (MQ=255)
                                    gACGCAGCATGCACCCCGGTGGAAATTAATGCACTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGt                               >  1:1362024/1‑71 (MQ=255)
                                       gcagcaTGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGtttt                            >  1:1606430/1‑71 (MQ=255)
                                       gcagcaTGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGttt                             >  1:2862587/1‑70 (MQ=255)
                                        cagcaTGCACCCCGGTGGAAATTAATGCACTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtc                           <  1:4872986/71‑1 (MQ=255)
                                         agcaTGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtca                          >  1:3361746/1‑71 (MQ=255)
                                         agcaTGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtca                          >  1:2276154/1‑71 (MQ=255)
                                         agcaTGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtca                          >  1:3033666/1‑71 (MQ=255)
                                           caTGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcatc                        <  1:3650808/71‑1 (MQ=255)
                                           caTGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcat                         >  1:3035468/1‑70 (MQ=255)
                                             tGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcatcat                      <  1:1229090/71‑1 (MQ=255)
                                             tGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcatcat                      <  1:4598664/71‑1 (MQ=255)
                                             tGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcatcat                      <  1:4111211/71‑1 (MQ=255)
                                             tGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcatcat                      <  1:3835069/71‑1 (MQ=255)
                                             tGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcatcat                      <  1:2334461/71‑1 (MQ=255)
                                             tGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcatcat                      <  1:3413175/71‑1 (MQ=255)
                                              gCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcatcat                      >  1:3160029/1‑70 (MQ=255)
                                               cACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcatcatca                    >  1:3095925/1‑71 (MQ=255)
                                               cACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcatcatca                    >  1:4715919/1‑71 (MQ=255)
                                               cACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcatcatca                    >  1:4721648/1‑71 (MQ=255)
                                                  cccGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGtt                              <  1:3009346/58‑1 (MQ=255)
                                                  cccGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGtt                              <  1:3952680/58‑1 (MQ=255)
                                                  cccGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGtt                              <  1:2222467/58‑1 (MQ=255)
                                                  cccGGTGGAAATTAATGCACTGGCGGCAATGGCACAGCACAGAAGATGTTTaa                                   <  1:1897887/53‑1 (MQ=255)
                                                  cccGGTGGAAATTAATGCACTGGCGGCAATGGCACAGCACAGAAGATGTTTaa                                   <  1:4630828/53‑1 (MQ=255)
                                                   ccGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACa                                 >  1:2809302/1‑54 (MQ=255)
                                                   ccGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACa                                 >  1:4681674/1‑54 (MQ=255)
                                                   ccGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACa                                 >  1:366386/1‑54 (MQ=255)
                                                   ccGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACa                                 >  1:5042696/1‑54 (MQ=255)
                                                   ccGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTAc                >  1:4133627/1‑71 (MQ=255)
                                                   ccGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTAc                >  1:4300237/1‑71 (MQ=255)
                                                   ccGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTAc                >  1:1271866/1‑71 (MQ=255)
                                                    cGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACagaa                                            <  1:4686469/42‑1 (MQ=255)
                                                    cGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGtt                              <  1:2623994/56‑1 (MQ=255)
                                                    cGGTGGAAATTAATGCACTGGCGGCAATGGCACAGCACAGAAGATGTTTAACa                                 >  1:2537951/1‑53 (MQ=255)
                                                    cGGTGGAAATTAATGCACTGGCGGCAATGGCACAGCACAGAAGATGTTTAACa                                 >  1:3409856/1‑53 (MQ=255)
                                                    cGGTGGAAATTAATGCACTGGCGGCAATGGCACAGCACAGAAGATGTTTAACa                                 >  1:4147154/1‑53 (MQ=255)
                                                    cGGTGGAAATTAATGCACTGGCGGCAATGGCACAGCACAGAAGATGTTTAACa                                 >  1:1677385/1‑53 (MQ=255)
                                                     ggTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACa                                 <  1:3639544/52‑1 (MQ=255)
                                                      gTGGAAATTAATTCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCa             <  1:835221/71‑1 (MQ=255)
                                                      gTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGttt                                     <  1:1919490/47‑1 (MQ=255)
                                                      gTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCa             <  1:766292/71‑1 (MQ=255)
                                                      gTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCa             <  1:416726/71‑1 (MQ=255)
                                                      gTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCa             <  1:2989601/71‑1 (MQ=255)
                                                       tGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCaa            <  1:4916977/71‑1 (MQ=255)
                                                       tGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCaa            <  1:4432939/71‑1 (MQ=255)
                                                       tGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCaa            <  1:4508629/71‑1 (MQ=255)
                                                       tGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCaa            <  1:2043002/71‑1 (MQ=255)
                                                       tGGAAATTAATGCACTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAg                                <  1:4743339/51‑1 (MQ=255)
                                                       tGGAAATTAATGCACTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAg                                <  1:3789866/51‑1 (MQ=255)
                                                        ggAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcat                         >  1:3759408/1‑57 (MQ=255)
                                                         gAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtcatcat                      <  1:988466/59‑1 (MQ=255)
                                                         gAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCAAgg          >  1:5138400/1‑71 (MQ=255)
                                                          aaaTTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtc                           <  1:759714/53‑1 (MQ=255)
                                                          aaaTTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTtc                           <  1:2075341/53‑1 (MQ=255)
                                                           aaTTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCAAGGTg        <  1:1184046/71‑1 (MQ=255)
                                                           aaTTAATGCGCTGGCGGAAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCAAGGTg        <  1:2043603/71‑1 (MQ=255)
                                                            aTTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAg                                >  1:4283266/1‑46 (MQ=255)
                                                            aTTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCaa            <  1:2927845/66‑1 (MQ=255)
                                                            aTTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCaa            <  1:1407242/66‑1 (MQ=255)
                                                            aTTAATGCACTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCAAGGTgg       <  1:700657/71‑1 (MQ=255)
                                                             ttAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCAAGGTgg       >  1:1069946/1‑70 (MQ=255)
                                                             ttAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCAAGGTgg       >  1:4715012/1‑70 (MQ=255)
                                                             ttAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCAAGGTGGa      <  1:937025/71‑1 (MQ=255)
                                                              tAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCAAGGTGGaa     >  1:4742944/1‑71 (MQ=255)
                                                               aaTGCGCTTGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCAAGGTGGAAt    >  1:2817666/1‑71 (MQ=255)
                                                               aaTGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTa                 >  1:2557363/1‑58 (MQ=255)
                                                                aTGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCAAGGTGGTAtt   <  1:2624951/71‑1 (MQ=255)
                                                                 tGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCAAGGTGGAATtg  <  1:1969454/71‑1 (MQ=255)
                                                                    |                                                                   
AGTTCGCTGGCGGCGCTGGAGAGCGCATCTTTCCAGGACGCAGCATGCACCCCGGTGGAAATTAATGCGCTGGCGGCAATGGCACAGCACAGAAGATGTTTAACAGTTTTCATCATCATTACTCAAGGTGGAATTG  >  W3110S.gb/4604756‑4604891

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A