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 F17 I0 R2 276 45.3 3729697 93.0% 3468618 60.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,918,430 G→A 33.7% L264L (CTG→TTG)  insK ← IS150 conserved protein InsB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,918,4300GA33.7% 109.6 / 81.1 89L264L (CTG→TTG) insKIS150 conserved protein InsB
Reads supporting (aligned to +/- strand):  ref base G (33/26);  new base A (13/17);  total (46/43)
Fisher's exact test for biased strand distribution p-value = 2.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01

CAGTTAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCGCT  >  W3110S.gb/3918365‑3918490
                                                                 |                                                            
cAGTTAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCt                                                           <  1:1925536/69‑1 (MQ=255)
    tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAtt                                                       >  1:1269534/1‑69 (MQ=255)
    tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAtt                                                       >  1:2151489/1‑69 (MQ=255)
    tAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAAtt                                                       >  1:2156067/1‑69 (MQ=255)
            aGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTctgct                                               >  1:1794707/1‑69 (MQ=255)
             ggCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTctgctg                                              >  1:1765119/1‑69 (MQ=255)
                atatAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgt                                             >  1:824733/1‑67 (MQ=255)
                   taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATtcttct                                                  >  1:2881593/1‑59 (MQ=255)
                   taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATtcttct                                                  >  1:1681145/1‑59 (MQ=255)
                   taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtag                                        >  1:2129704/1‑69 (MQ=255)
                   taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtag                                        >  1:2015613/1‑69 (MQ=255)
                   taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtag                                        >  1:557645/1‑69 (MQ=255)
                   taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtag                                        >  1:661827/1‑69 (MQ=255)
                   taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtag                                        >  1:1431513/1‑69 (MQ=255)
                   taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtag                                        >  1:2814963/1‑69 (MQ=255)
                   taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtag                                        >  1:1191314/1‑69 (MQ=255)
                   taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtag                                        >  1:3139499/1‑69 (MQ=255)
                   taGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAAttc                                                      >  1:797941/1‑55 (MQ=255)
                    aGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTaa                                                         <  1:2784745/51‑1 (MQ=255)
                    aGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTaa                                                         <  1:3496531/51‑1 (MQ=255)
                    aGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTaa                                                         <  1:1334508/51‑1 (MQ=255)
                     ggTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGCCTAATTCTTCTGCTGTTgtagt                                       >  1:2109294/1‑68 (MQ=255)
                     ggTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTctg                                                 <  1:2685542/58‑1 (MQ=255)
                     ggTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTctg                                                 <  1:2212112/58‑1 (MQ=255)
                             tCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttg                                           <  1:540988/56‑1 (MQ=255)
                             tCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttg                                           <  1:762621/56‑1 (MQ=255)
                             tCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               >  1:1639383/1‑68 (MQ=255)
                             tCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAata                               <  1:925043/68‑1 (MQ=255)
                             tCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCaa                                 <  1:2366611/66‑1 (MQ=255)
                             tCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCaa                                 <  1:2085273/66‑1 (MQ=255)
                             tCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCaa                                 <  1:2708721/66‑1 (MQ=255)
                             tCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCaa                                 <  1:2982810/66‑1 (MQ=255)
                             tCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCaa                                 <  1:3102447/66‑1 (MQ=255)
                             tCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCaa                                 <  1:1059136/66‑1 (MQ=255)
                             tCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCaa                                 <  1:842590/66‑1 (MQ=255)
                             tCCGATATTCAATTGGAGTCAGACCTTTTAATTT‑AGGCTAATTCTTCTGCTGTTGTAGTATTCAatat                              >  1:3460380/1‑68 (MQ=255)
                                gATATTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAatatat                            <  1:2347656/68‑1 (MQ=255)
                                  tatTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTc                          >  1:3714370/1‑68 (MQ=255)
                                  tatTCAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTc                          >  1:2124600/1‑68 (MQ=255)
                                   atTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttg                                           <  1:1911936/50‑1 (MQ=255)
                                   atTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttg                                           <  1:868478/50‑1 (MQ=255)
                                   atTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttg                                           <  1:2799892/50‑1 (MQ=255)
                                   atTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttg                                           <  1:1350743/50‑1 (MQ=255)
                                   atTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttg                                           <  1:1518465/50‑1 (MQ=255)
                                   atTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttg                                           <  1:1715237/50‑1 (MQ=255)
                                   atTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttg                                           <  1:451676/50‑1 (MQ=255)
                                   atTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttg                                           <  1:2175844/50‑1 (MQ=255)
                                    ttCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGt                       <  1:3538786/69‑1 (MQ=255)
                                    ttCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGt                       <  1:2211600/69‑1 (MQ=255)
                                      cAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTa                      <  1:918835/68‑1 (MQ=255)
                                      cAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGt                       >  1:2567603/1‑67 (MQ=255)
                                      cAATTGGAGTCAGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGt                       >  1:964986/1‑67 (MQ=255)
                                         ttGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAg                  <  1:1500964/69‑1 (MQ=255)
                                         ttGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAg                  >  1:2032345/1‑69 (MQ=255)
                                           ggAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttgt                                          <  1:3374324/43‑1 (MQ=255)
                                           ggAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttgt                                          <  1:976825/43‑1 (MQ=255)
                                           ggAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttgt                                          <  1:1927558/43‑1 (MQ=255)
                                           ggAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCtgttgt                                          <  1:236477/43‑1 (MQ=255)
                                           ggAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCa                >  1:375083/1‑69 (MQ=255)
                                           ggAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCa                >  1:138909/1‑69 (MQ=255)
                                           ggAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCa                >  1:1465776/1‑69 (MQ=255)
                                           ggAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCa                >  1:3558317/1‑69 (MQ=255)
                                            gAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCAt               >  1:3296901/1‑69 (MQ=255)
                                              gTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATcc             >  1:1165260/1‑69 (MQ=255)
                                                cAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCa                >  1:2109302/1‑64 (MQ=255)
                                                 aGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTc          >  1:670895/1‑69 (MQ=255)
                                                 aGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTgta                                         >  1:775388/1‑38 (MQ=255)
                                                 aGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTgta                                         >  1:3629687/1‑38 (MQ=255)
                                                 aGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTgta                                         >  1:3674841/1‑38 (MQ=255)
                                                 aGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTgta                                         >  1:1377168/1‑38 (MQ=255)
                                                 aGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTgta                                         >  1:556937/1‑38 (MQ=255)
                                                 aGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGc                 <  1:612235/62‑1 (MQ=255)
                                                 aGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGc                 <  1:3031600/62‑1 (MQ=255)
                                                 aGACCTTTTAATTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGc                 <  1:2638263/62‑1 (MQ=255)
                                                 aGACCTTTTAATTTCAAGCTAATTCTTCAGCAGTTgta                                         >  1:2238580/1‑38 (MQ=25)
                                                   aCCTTTTAATTTCAGGCTAATTCTTCTGCtgttgt                                          <  1:2556950/35‑1 (MQ=255)
                                                    ccTTTTAATTTCAAGCTAATTCTTCTGCTGTTgtag                                        <  1:827246/36‑1 (MQ=255)
                                                     cTTTTAATTTCAGGCTAATTCTTCTGCTGTTgtag                                        <  1:108682/35‑1 (MQ=255)
                                                     cTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGtt      >  1:3097997/1‑69 (MQ=255)
                                                        ttAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTaa                     <  1:1332333/51‑1 (MQ=255)
                                                        ttAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCg    >  1:317170/1‑68 (MQ=255)
                                                          aaTTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCaa                                 <  1:2210894/37‑1 (MQ=255)
                                                          aaTTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCaa                                 <  1:1637824/37‑1 (MQ=255)
                                                          aaTTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCGCt  >  1:1804165/1‑68 (MQ=255)
                                                          aaTTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCGCt  >  1:1578957/1‑68 (MQ=255)
                                                          aaTTTCAGGCTAATTCTTATGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCGCt  >  1:3720728/1‑68 (MQ=255)
                                                          aaTTTCAAGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCGCt  >  1:2843064/1‑68 (MQ=255)
                                                           aTTTCAGGCTAATTCTTCTGCTGTGGTAGTATTCaa                                 <  1:1816020/36‑1 (MQ=255)
                                                              tCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGt       >  1:633924/1‑59 (MQ=255)
                                                                 |                                                            
CAGTTAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCGCT  >  W3110S.gb/3918365‑3918490

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