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
A3 F2 I1 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA Exported 834,197 C→T 21.0% H885H (CAC→CAT) ‡ narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported834,1970CT21.0% 109.4 / 23.5 57H885H (CAC→CAT) ‡narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (21/24);  new base T (6/6);  total (27/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.91e-01

CAGCCGCTGGATGTGAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATG  >  Exported/834129‑834263
                                                                    |                                                                  
cAGCCGCTGGATGTGAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACAt                                                                  <  1:4363823/71‑1 (MQ=255)
cAGCCGCTGGATGTGAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACAt                                                                  <  1:2022595/71‑1 (MQ=255)
 aGCCGCTGGATGTGAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACAt                                                                  >  1:160659/1‑70 (MQ=255)
    cGCTGGATGTGAAAGACTGGAAAAAAGGCGAGTGCCACCTGATCCCAGGTAAAACCGCGCCACACATTa                                                                >  1:4560834/1‑69 (MQ=255)
     gCTGGATGTGAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATgg                                                             >  1:1512062/1‑71 (MQ=255)
         gATGTGAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCg                                                          >  1:1450425/1‑70 (MQ=255)
            gtgAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTag                                                       <  1:3745983/70‑1 (MQ=255)
            gtgAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTag                                                       <  1:4649663/70‑1 (MQ=255)
              gAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTAt                                                               <  1:5623542/60‑1 (MQ=255)
              gAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTAt                                                               <  1:3166538/60‑1 (MQ=255)
              gAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTAt                                                               <  1:3295580/60‑1 (MQ=255)
               aaaGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAgcg                                                   >  1:2738305/1‑71 (MQ=255)
                aaGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAgcgc                                                  <  1:242395/71‑1 (MQ=255)
                 aGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAgcgc                                                  >  1:5349412/1‑70 (MQ=255)
                     tGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTa                                             >  1:2027666/1‑71 (MQ=255)
                         gcaaaGGCGAATGCGATCTGATTCCAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTAccct                                         >  1:2952907/3‑70 (MQ=255)
                          aaaaGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCgg                                        >  1:220715/1‑71 (MQ=255)
                           aaaGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTag                                                       <  1:4668124/55‑1 (MQ=255)
                           aaaGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTag                                                       <  1:3944940/55‑1 (MQ=255)
                            aaGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTAt                                            <  1:5422594/65‑1 (MQ=255)
                             aGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTagag                                                     >  1:3313046/1‑55 (MQ=255)
                             aGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTagag                                                     >  1:4913471/1‑55 (MQ=255)
                             aGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTagag                                                     >  1:298110/1‑55 (MQ=255)
                             aGGCGACTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTaga                                                      >  1:739382/1‑54 (MQ=255)
                              ggCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGa                                     >  1:1320910/1‑70 (MQ=255)
                               gCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACt                                   <  1:2308008/71‑1 (MQ=255)
                               gCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACt                                   <  1:2612768/71‑1 (MQ=255)
                                  aGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTAc                                <  1:4876532/71‑1 (MQ=255)
                                  aGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTAc                                <  1:1073281/71‑1 (MQ=255)
                                   gTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTa                                 >  1:5092015/1‑69 (MQ=255)
                                   gTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTAc                                >  1:1805810/1‑70 (MQ=255)
                                        atcTGATTCCAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAAc                            <  1:1171900/67‑1 (MQ=255)
                                        atcTGATTCCAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAAc                            <  1:1531459/67‑1 (MQ=255)
                                        atcTGATTCCAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAAc                            <  1:1759713/67‑1 (MQ=255)
                                           tGATCCCAGGTAAAACCGCGCCACACATTATGGTc                                                           <  1:2240234/35‑1 (MQ=255)
                                           tGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATcc                                          <  1:230778/52‑1 (MQ=255)
                                           tGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAAc                            <  1:3983531/66‑1 (MQ=255)
                                             aTCCCAGGTAAAACCGCGCCACACATTATGGTCGTag                                                       <  1:5539480/37‑1 (MQ=255)
                                             aTCCCAGGTAAAACCGCGCCACACATTATGGTCGTATAGCGCGATTATCCGGCGACTTACGAACGCtt                        <  1:1439717/68‑1 (MQ=255)
                                             aTCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCtt                        <  1:1762731/68‑1 (MQ=255)
                                             aTCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTAc                     >  1:3137129/1‑71 (MQ=255)
                                             aTCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTAc                     >  1:1664951/1‑71 (MQ=255)
                                                 cAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACctct                 <  1:2961830/71‑1 (MQ=255)
                                                 cAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTacc                                           >  1:3652708/1‑43 (MQ=255)
                                                  aGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTa                >  1:4131261/1‑71 (MQ=255)
                                                  aGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGc                          <  1:2274748/61‑1 (MQ=255)
                                                  aGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTACctcgc                <  1:1793489/71‑3 (MQ=255)
                                                   ggTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGaa                             >  1:4401786/1‑57 (MQ=255)
                                                    gTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCttt                       <  1:3205612/62‑1 (MQ=255)
                                                      aaaaCCTCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTACCTCGCTCgg            >  1:3373877/1‑71 (MQ=255)
                                                      aaaaCCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTACCTCGCTCgg            >  1:2028724/1‑71 (MQ=255)
                                                      aaaaCCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTACCTCGCTCgg            <  1:537943/71‑1 (MQ=255)
                                                      aaaaCCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTACCTCGCTCgg            >  1:4059875/1‑71 (MQ=255)
                                                      aaaaCCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTACCTCGCTCgg            >  1:3264816/1‑71 (MQ=255)
                                                            gcgcCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTAc                     >  1:2682170/1‑56 (MQ=255)
                                                            gcgcCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTAc                     >  1:2475642/1‑56 (MQ=255)
                                                            gcgcCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCt      <  1:151129/71‑1 (MQ=255)
                                                                cacacaTTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTAc                     >  1:1043999/1‑52 (MQ=255)
                                                                  cacaTTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACctc                  <  1:5323215/53‑1 (MQ=255)
                                                                   acaTTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACctct                 <  1:38355/53‑1 (MQ=255)
                                                                   acaTTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATg  >  1:2989700/1‑68 (MQ=255)
                                                                    caTTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTa                >  1:3775983/1‑53 (MQ=255)
                                                                    |                                                                  
CAGCCGCTGGATGTGAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATG  >  Exported/834129‑834263

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