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 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,362,267 T→G 26.2% E344A (GAA→GCA)  cadA ← lysine decarboxylase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,362,2670TG26.2% 89.6 / 69.7 84E344A (GAA→GCA) cadAlysine decarboxylase 1
Reads supporting (aligned to +/- strand):  ref base T (32/30);  new base G (11/11);  total (43/41)
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

TTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCA  >  W3110S.gb/4362198‑4362333
                                                                     |                                                                  
ttGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTc                                                                   >  1:3027634/1‑71 (MQ=255)
 tgtgAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACATTCg                                                                  >  1:345580/1‑71 (MQ=255)
     aGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTaaa                                                              >  1:3533175/1‑71 (MQ=255)
      gTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAAt                                                             <  1:745039/71‑1 (MQ=255)
              ggTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTgaga                                                     <  1:403796/71‑1 (MQ=255)
              ggTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTga                                                       <  1:1865866/69‑1 (MQ=255)
                 ttCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGaa                                                    <  1:2622330/69‑1 (MQ=255)
                  tCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGt                                                  <  1:2700640/70‑1 (MQ=255)
                    gTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCg                                                           >  1:4429492/1‑59 (MQ=255)
                     tAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTg                                                <  1:318287/69‑1 (MQ=255)
                     tAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTg                                                <  1:944055/69‑1 (MQ=255)
                     tAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTg                                                <  1:897446/69‑1 (MQ=255)
                      aaaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCATCGTAAATCGGTGAGAAGTTGgt                                              <  1:2152600/70‑1 (MQ=255)
                       aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGgtgt                                            <  1:95774/71‑1 (MQ=255)
                       aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGgtgt                                            <  1:2382754/71‑1 (MQ=255)
                       aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGgtgt                                            <  1:3732701/71‑1 (MQ=255)
                       aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGgtg                                             >  1:440510/1‑70 (MQ=255)
                       aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGgtg                                             >  1:2378667/1‑70 (MQ=255)
                       aaTCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGgtg                                             >  1:150241/1‑70 (MQ=255)
                          cACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGt                                                  <  1:1240166/62‑1 (MQ=255)
                          cACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTgg                                               >  1:2750027/1‑65 (MQ=255)
                          cACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAg                                         >  1:351177/1‑71 (MQ=255)
                          cACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAg                                                   >  1:4082043/1‑61 (MQ=255)
                           aCTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAgg                                        <  1:3590014/71‑1 (MQ=255)
                           aCTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAgg                                        <  1:1377389/71‑1 (MQ=255)
                               tCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAAt                                                             >  1:4373899/1‑46 (MQ=255)
                               tCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAAt                                                             >  1:2266072/1‑46 (MQ=255)
                                 ccTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTa                                                                <  1:2441108/41‑1 (MQ=255)
                                 ccTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTa                                           >  1:913984/1‑62 (MQ=255)
                                 ccTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCa                                      <  1:2832397/67‑1 (MQ=255)
                                    tCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGgtg                                             <  1:5637/57‑1 (MQ=255)
                                    tCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGgtg                                             <  1:1622679/57‑1 (MQ=255)
                                    tCTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGgtg                                             <  1:4089303/57‑1 (MQ=255)
                                     cTACACGGCCACCGCTCATACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCAcgcg                              >  1:2051286/1‑71 (MQ=255)
                                      tACACGGCCACCGCTCATACCGCATTTACCTTCGTaa                                                               <  1:2093888/37‑1 (MQ=255)
                                      tACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCgg                                                          >  1:320922/1‑42 (MQ=255)
                                      tACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCAc                                     >  1:2152097/1‑63 (MQ=255)
                                      tACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCAcgcg                              >  1:1005541/1‑70 (MQ=255)
                                      tACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCAcgcg                              >  1:4072850/1‑70 (MQ=255)
                                       acacGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCAcgcg                              >  1:392972/1‑69 (MQ=255)
                                         acGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCa                                      >  1:588352/1‑59 (MQ=255)
                                         acGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCAcgcg                              <  1:4547801/67‑1 (MQ=255)
                                           ggCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCa                        <  1:3747651/71‑1 (MQ=255)
                                            gCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaa                       <  1:1204597/71‑1 (MQ=255)
                                            gCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaa                       <  1:4259751/71‑1 (MQ=255)
                                             ccACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaa                       <  1:4264961/70‑1 (MQ=255)
                                                ccGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtg                   <  1:4504716/71‑1 (MQ=255)
                                                 cGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAg                     >  1:1057398/1‑68 (MQ=255)
                                                 cGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAg                     >  1:1950440/1‑68 (MQ=255)
                                                  gCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaaa                      >  1:4249669/1‑66 (MQ=255)
                                                  gCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtgga                 >  1:321880/1‑71 (MQ=255)
                                                  gCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtgga                 >  1:219708/1‑71 (MQ=255)
                                                  gCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtgga                 >  1:3328557/1‑71 (MQ=255)
                                                  gCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtgga                 <  1:430731/71‑1 (MQ=255)
                                                  gCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtgga                 >  1:4071783/1‑71 (MQ=255)
                                                  gCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtgga                 >  1:324005/1‑71 (MQ=255)
                                                   cTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTaa                                          >  1:3113758/1‑45 (MQ=255)
                                                     cATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTaa                                          >  1:4277539/1‑43 (MQ=255)
                                                      aTACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtggatg               <  1:4278660/69‑1 (MQ=255)
                                                      aTACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtggatgga             >  1:3431558/1‑71 (MQ=255)
                                                      aTACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtggatg               <  1:4077594/69‑1 (MQ=255)
                                                       tACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGTTGTAAGGc                                       <  1:3099120/44‑1 (MQ=255)
                                                       tACCGCATTTACCTGCGTAAATCGGTGAGAAGTTGgtgt                                            <  1:501801/39‑1 (MQ=255)
                                                        aCCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaa                       <  1:3066107/59‑1 (MQ=255)
                                                        aCCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtgga                 >  1:1653899/1‑65 (MQ=255)
                                                         ccGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTaa                                          >  1:2715993/1‑39 (MQ=255)
                                                         ccGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGAttt          <  1:2119036/71‑1 (MQ=255)
                                                         ccGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGAttt          >  1:1301075/1‑71 (MQ=255)
                                                         ccGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGAttt          >  1:464296/1‑71 (MQ=255)
                                                         ccGCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGAttt          >  1:2307705/1‑71 (MQ=255)
                                                          cGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGAttt          >  1:2519216/1‑70 (MQ=255)
                                                           gCATTTACCTGCGTAAATCGGTGAGAAGTTGgtgt                                            <  1:2633605/35‑1 (MQ=255)
                                                           gCATTTACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTca        >  1:362551/1‑71 (MQ=255)
                                                             aTTTACCTGCGTAAATCGGTGAGAAGTTGGTTTAAGGCACCCACGCGGAGTCAATGtggatg               <  1:2400324/62‑1 (MQ=255)
                                                              tttACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaa                       <  1:128408/53‑1 (MQ=255)
                                                              tttACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCaa                       <  1:2872460/53‑1 (MQ=255)
                                                                tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtggatgga             >  1:1789949/1‑61 (MQ=255)
                                                                tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATc    <  1:2949794/70‑1 (MQ=255)
                                                                tACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATc    >  1:1797227/1‑70 (MQ=255)
                                                                tACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa                                  >  1:3218428/1‑40 (MQ=255)
                                                                tACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCa                                  >  1:3800615/1‑40 (MQ=255)
                                                                tACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGtg                   <  1:2055910/55‑1 (MQ=255)
                                                                tACCTGCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATc    >  1:4059977/1‑70 (MQ=255)
                                                                  ccTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCa  <  1:1956425/70‑1 (MQ=255)
                                                                     |                                                                  
TTGTGAGTGGACTGGGTTTCGTAAATCACTTTCCCTTCTACACGGCCACCGCTCATACCGCATTTACCTTCGTAAATCGGTGAGAAGTTGGTGTAAGGCACCCACGCGGAGTCAAAGTGGATGGATTTCACATCCA  >  W3110S.gb/4362198‑4362333

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