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 1,099,547 C→T 47.5% A143V (GCC→GTC)  ycdX → predicted zinc‑binding hydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,099,5470CT47.5% 9.9 / 82.5 59A143V (GCC→GTC) ycdXpredicted zinc‑binding hydrolase
Reads supporting (aligned to +/- strand):  ref base C (17/14);  new base T (17/11);  total (34/25)
Fisher's exact test for biased strand distribution p-value = 7.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.80e-01

CTATCGCCAGCGGCAATGTGCATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCAATAATTCCTCATTTTTACACTC  >  W3110S.gb/1099478‑1099613
                                                                     |                                                                  
cTATCGCCAGCGGCAATGTGCATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGcc                                                                   <  1:2689715/71‑1 (MQ=255)
cTATCGCCAGCGGCAATGTGCATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGcc                                                                   <  1:4291345/71‑1 (MQ=255)
  aTCGCCAGCGGCAATGTGCATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGt                                                                 >  1:5078934/1‑71 (MQ=255)
   tCGCCAGCGGCAATGTGCATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGTCGtt                                                                >  1:75379/1‑71 (MQ=255)
               aTGTGCATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGcc                                                    <  1:3449716/71‑1 (MQ=255)
               aTGTGCATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGcc                                                    <  1:779048/71‑1 (MQ=255)
               aTGTGCATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGcc                                                    <  1:1445239/71‑1 (MQ=255)
               aTGTGCATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGcc                                                    <  1:2659383/71‑1 (MQ=255)
                  tgCATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGTCg                                                                  <  1:3581478/54‑1 (MQ=255)
                  tgCATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCcgc                                                  >  1:1796981/1‑70 (MQ=255)
                    cATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGaa                                               <  1:1573273/71‑1 (MQ=255)
                    cATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGa                                                <  1:802690/70‑1 (MQ=255)
                       ataataAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGTCGTTGCTGa                                                           <  1:1885757/56‑1 (MQ=255)
                        taataaGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTg                                                               >  1:643167/1‑51 (MQ=255)
                         aataaGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAagc                                                        >  1:1920996/1‑57 (MQ=255)
                         aataaGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAagc                                                        >  1:3737956/1‑57 (MQ=255)
                          ataaGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGTCGTTg                                                               >  1:1819146/1‑49 (MQ=255)
                          ataaGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGTCGTTGCTGAagcagc                                                     >  1:237207/1‑59 (MQ=255)
                          ataaGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATc                                          <  1:1215645/70‑1 (MQ=255)
                           taaGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGc                                                              >  1:4633102/1‑49 (MQ=255)
                           taaGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGaaa                                              >  1:219448/1‑65 (MQ=255)
                           taaGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGaaa                                              >  1:4791473/1‑65 (MQ=255)
                           taaGCCATCCCGGAAATCCCAAATATGAAATAGATATGAAAGCCGTTGc                                                              >  1:3843036/1‑49 (MQ=255)
                            aaGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGc                                                                    >  1:3977592/1‑42 (MQ=255)
                                  tCCCGGAAATCCCAAATATGAAATAGATGTGAAAGTCGTTGCTGa                                                           <  1:2799441/45‑1 (MQ=255)
                                    ccGGAAATCCCAAATATGAAATAGATGTGAAAGTCGtt                                                                >  1:592088/1‑38 (MQ=255)
                                    ccGGAAATCCCAAATATGAAATAGATGTGAAAGTCGTTGCTGAagcagc                                                     >  1:72726/1‑49 (MQ=255)
                                    ccGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTg                                                               >  1:1149638/1‑39 (MQ=255)
                                    ccGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCt                                <  1:830305/70‑1 (MQ=255)
                                    ccGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCt                                <  1:3596424/70‑1 (MQ=255)
                                    ccGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTg                               >  1:4696637/1‑71 (MQ=255)
                                         aaTCCCAAATATGAAATAGATGTGAAAGTCGTTGCTGAagc                                                        >  1:2378819/1‑41 (MQ=255)
                                          aTCCCAAATATGAAATAGATGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAg                                        >  1:573788/1‑56 (MQ=255)
                                          aTCCCAAATATGAAATAGATGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAg                                        >  1:1469327/1‑56 (MQ=255)
                                             ccAAATATGAAATAGATGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGaa                            <  1:3534648/65‑1 (MQ=255)
                                             ccAAATATGAAATAGATGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaat                      <  1:666781/71‑1 (MQ=255)
                                             ccAAATATGAAATAGATGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaat                      <  1:1299359/71‑1 (MQ=255)
                                             ccAAATATGAAATAGATGTGAAAGCCGTTGCTGAagca                                                       >  1:3221270/1‑38 (MQ=255)
                                                aaTATGAAATAGATGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaataat                   >  1:4247066/1‑71 (MQ=255)
                                                aaTATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaataat                   >  1:1721463/1‑71 (MQ=255)
                                                aaTATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaataa                    <  1:3356597/70‑1 (MQ=255)
                                                 atatGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaat                      <  1:2739935/67‑1 (MQ=255)
                                                    tGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCAATAATTcc                <  1:1334148/70‑1 (MQ=255)
                                                    tGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCAATAATTcc                <  1:1598486/70‑1 (MQ=255)
                                                       aaTAGATGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaat                      <  1:3281552/61‑1 (MQ=255)
                                                       aaTAGATGTGAAAGTCGTTGCTGAAGCAGC‑‑CGAAACATCAGGTGGCGCTGGAAATCaat                      <  1:4647155/59‑1 (MQ=255)
                                                           gATGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaat                      <  1:4679788/57‑1 (MQ=255)
                                                            aTGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaa                       >  1:992394/1‑55 (MQ=255)
                                                            aTGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaa                       >  1:4957326/1‑55 (MQ=255)
                                                            aTGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaa                       >  1:403586/1‑55 (MQ=255)
                                                            aTGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaa                       >  1:366893/1‑55 (MQ=255)
                                                            aTGTGAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaa                       >  1:2999711/1‑55 (MQ=255)
                                                            aTGTGAAAGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCAATAATTCCTCATTTTTa       <  1:2647427/71‑1 (MQ=255)
                                                              gtgAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCAATAATTcc                >  1:381591/1‑60 (MQ=255)
                                                              gtgAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCAATAATTcc                >  1:2909745/1‑60 (MQ=255)
                                                              gtgAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCAATAATTcc                >  1:3139310/1‑60 (MQ=255)
                                                              gtgAAAGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCAATAATTCCTCATTTTTaca     >  1:4374772/1‑71 (MQ=255)
                                                               tgAAAGTCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCaataa                    <  1:2380978/55‑1 (MQ=255)
                                                                gAAAGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCAATAATTCCTCATTTTTac      >  1:230132/1‑68 (MQ=255)
                                                                 aaaGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCAATAATTCCTCATTTTTACACt   >  1:29063/1‑70 (MQ=255)
                                                                 aaaGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCAATAATTCCTCATTTTTACACt   >  1:3702885/1‑70 (MQ=255)
                                                                 aaaGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCAATAATTCCTCATTTTTACACTc  <  1:1126492/71‑1 (MQ=255)
                                                                     |                                                                  
CTATCGCCAGCGGCAATGTGCATATAATAAGCCATCCCGGAAATCCCAAATATGAAATAGATGTGAAAGCCGTTGCTGAAGCAGCCGCGAAACATCAGGTGGCGCTGGAAATCAATAATTCCTCATTTTTACACTC  >  W3110S.gb/1099478‑1099613

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