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 F21 I0 R1 476 35.3 2812105 96.7% 2719305 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,927,326 G→A 75.0% V148M (GTG→ATG)  sdaC → predicted serine transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,927,3260GA75.0% 97.7 / 35.0 56V148M (GTG→ATG) sdaCpredicted serine transporter
Reads supporting (aligned to +/- strand):  ref base G (6/8);  new base A (17/25);  total (23/33)
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

AGCTTCATGTCTCACCAGCTGGGTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCGTGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTATTCTGGTATT  >  W3110S.gb/2927260‑2927393
                                                                  |                                                                   
aGCTTCATGTCTCACCAGCTGGGTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATggg                                                                 <  1:952321/71‑1 (MQ=255)
  cTTCATGTCTCACCAGCTGGGTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTa                                                               >  1:225872/1‑71 (MQ=255)
     cATGTCTCACCAGCTGGGTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGGTCCTGATCGTGGGTatg                                                             <  1:2167080/70‑1 (MQ=255)
     cATGTCTCACCAGCTGGGTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCGTGGGTatg                                                             <  1:1313259/70‑1 (MQ=255)
       tGTCTCACCAGCTGGGTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTatgatg                                                          <  1:755013/71‑1 (MQ=255)
       tGTCTCACCAGCTGGGTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTatgatg                                                          <  1:2402462/71‑1 (MQ=255)
             aCCAGCTGGGTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTataat                                                           <  1:2751015/64‑1 (MQ=255)
             aCCAGCTGGGTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGAcc                                                       <  1:2519572/68‑1 (MQ=255)
                aGCTGGGTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCGTGGGTATGATGACCATCGtt                                                 >  1:1314964/1‑71 (MQ=255)
                  cttggTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCg                                               <  1:2716639/68‑1 (MQ=255)
                   tGGGTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCg                                               >  1:927733/1‑70 (MQ=255)
                      gTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCGTGGGTATGATGACCATCGTTCGCTTc                                           <  1:1232222/71‑1 (MQ=255)
                         tGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCGTGGGTat                                                              <  1:2753073/49‑1 (MQ=255)
                          gACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGT‑‑‑ATGACCATCGTTCGCTTCGGTGa                                      >  1:897896/1‑69 (MQ=255)
                           aCGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCGTGGGTAtgatga                                                         >  1:484862/1‑52 (MQ=255)
                           aCGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGt                                        >  1:2600631/1‑69 (MQ=255)
                           aCGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGt                                        >  1:1968794/1‑69 (MQ=255)
                            cGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAg                                     <  1:514550/71‑1 (MQ=255)
                              ccACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCa                                   <  1:2513670/71‑1 (MQ=255)
                               cACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCGTGGGTATGATGACCATCGTTCGCTTCGGTGAGCa                                   <  1:2568081/70‑1 (MQ=255)
                               cACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAg                                  <  1:2053281/71‑1 (MQ=255)
                               cACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAg                                  <  1:188783/71‑1 (MQ=255)
                               cACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAg                                  <  1:2566203/71‑1 (MQ=255)
                                aCCGCCGCGTGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAg                                     >  1:2749324/1‑67 (MQ=255)
                                  cgccgcGTGCGATTCTGTCGCTGATCCTGATCGTGGGTATGATGACCATCGTTCGCTTCGGTGa                                      >  1:1963349/1‑64 (MQ=255)
                                  cgccgcGTGCGATTCTGTCGCTGATCCTGATCGTGGGTATGATGACCATCGTTCGCTTCGGTGAGCAgatg                               <  1:1544852/71‑1 (MQ=255)
                                  cgccgcGTGCGATTCTGTCGCTGATCCTGATCGTGGGTATGATGACCATCGTTCGCTTCGGTGAGCAgatg                               <  1:1310186/71‑1 (MQ=255)
                                  cgccgcGTGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAgatg                               <  1:1776652/71‑1 (MQ=255)
                                      gcgTGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCg                           >  1:251608/1‑71 (MQ=255)
                                         tGCGATTCTGTCGCTGATCCTGATCATGGGTatgatg                                                          <  1:989871/37‑1 (MQ=255)
                                         tGCGATTCTGTCGCTGATCCTGATCATGGGTATGATGAc                                                        >  1:2612297/1‑39 (MQ=255)
                                             aTTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGc                    <  1:1950742/71‑1 (MQ=255)
                                             aTTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGc                    <  1:524721/71‑1 (MQ=255)
                                             aTTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGc                    <  1:1883971/71‑1 (MQ=255)
                                             aTTCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGc                    <  1:405131/71‑1 (MQ=255)
                                              ttCTGTCGCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCg                   <  1:641454/71‑1 (MQ=255)
                                               tCTGTAGCTGATCCTGAACATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGa                  >  1:2619639/1‑71 (MQ=255)
                                                     gCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGa               >  1:1509838/1‑68 (MQ=255)
                                                     gCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGa               >  1:248350/1‑68 (MQ=255)
                                                     gCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTa            <  1:930027/71‑1 (MQ=255)
                                                     gCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTa            <  1:918578/71‑1 (MQ=255)
                                                     gCTGATCCTGATCATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTa            >  1:1594405/1‑71 (MQ=255)
                                                         atcctgatcGTGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAg              <  1:2414537/65‑1 (MQ=255)
                                                           cctgatcGTGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCg                   >  1:2135092/1‑58 (MQ=255)
                                                           cctgatcGTGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGa               >  1:2188466/1‑62 (MQ=255)
                                                           cctgatcGTGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTATTCTgg      >  1:863375/1‑71 (MQ=255)
                                                           cctgatcATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTAtt          >  1:2014569/1‑67 (MQ=255)
                                                           cctgatcATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTATTCTgg      >  1:1867893/1‑71 (MQ=255)
                                                            ctgatcATGGGTATGATGACCATCGTTCTCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTATTCTgg      <  1:356030/70‑1 (MQ=255)
                                                            ctgatcATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTATTCTgg      >  1:1995596/1‑70 (MQ=255)
                                                               atcATGGGTATGATGACCATCGTTCGCTTCGGTGAGCa                                   <  1:756860/38‑1 (MQ=255)
                                                               atcATGGGTATGATGACCATCGTTCGCTTCGGTGAGCa                                   <  1:1477453/38‑1 (MQ=255)
                                                               atcATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTATTCTGGTa    <  1:432788/69‑1 (MQ=255)
                                                               atcATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTATTCTGGTa    <  1:2431369/69‑1 (MQ=255)
                                                               atcATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTATTCTGGTAtt  >  1:239399/1‑71 (MQ=255)
                                                               atcATGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTATTCTGGTAtt  >  1:504611/1‑71 (MQ=255)
                                                                  |                                                                   
AGCTTCATGTCTCACCAGCTGGGTATGACGCCACCGCCGCGTGCGATTCTGTCGCTGATCCTGATCGTGGGTATGATGACCATCGTTCGCTTCGGTGAGCAGATGATCGTTAAAGCGATGAGTATTCTGGTATT  >  W3110S.gb/2927260‑2927393

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A