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
A13 F121 I0 R1 43 32.8 695000 96.9% 673455 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 225,710 C→G 61.4% T266R (ACA→AGA)  murQ → possible sugar phosphate isomerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730225,7100CG61.4% 30.5 / 46.5 47T266R (ACA→AGA) murQpossible sugar phosphate isomerase
Reads supporting (aligned to +/- strand):  ref base C (8/10);  new base G (14/14);  total (22/25)
Fisher's exact test for biased strand distribution p-value = 7.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01

ACCTCATGATTGATGTTAAAGCAACCAATCAAAAACTGATCGACCGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGACAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGACAACCTTAGGAGGGATTTAAATGACCAAAGAACAACAACTTGCAGAAC  >  CP000730/225572‑225849
                                                                                                                                          |                                                                                                                                           
aCCTCATGATGGATGTTAAAGCAACCAATCAAAAACTGATCGACCGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGGGAAAGTTGCGagag                                                                                                                                           >  2:182296/1‑141 (MQ=255)
     aTGATTGATGTTAAAGCAACCAATCAAAAACTGATCGACCGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGACAGTTATg                                                                                                                                      <  2:276931/141‑1 (MQ=255)
        attgatGTTAAAGCAACCAATCAAAAACTGATCGACCGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGt                                                                                                                                   <  2:228941/141‑1 (MQ=255)
           gatGTTAAAGCAACCAATCAAAAACTGATCGACCGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGACAGTTATGGGTAtg                                                                                                                                >  1:231362/1‑141 (MQ=255)
            atGTTAGAACAACCATTGAAAAACTGTTCGGCTGTTCAGTGCGTATTATTCAAGAAATATGTGCAATCTTATATGATGTAGCAATGGCGTTATATCAGGTATCTGAGTATGATGTGATAGTTGCGTCAGTTATGGGTAtgt                                                                                                                               <  2:230256/141‑1 (MQ=255)
             tGTTAAAGCAACCAATCAAAAACTGATCGACCGTTCAGTGCGTATTACTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGACAGTTATGGGTAtgtg                                                                                                                              <  1:186305/141‑1 (MQ=255)
             cgcacacgaaaCCGATCAAAAACCGATCGACCGTTCAGTGCGTACTATTTAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTAtgtg                                                                                                                              <  2:329889/132‑1 (MQ=255)
                tAAAGCAACCAATCAAAAACTGATCGACCGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTgg                                                                                                                           <  1:253292/141‑1 (MQ=255)
                           aTCAAAAACTGATCGACCGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAgg                                                                                                                >  2:227100/1‑141 (MQ=255)
                            tCAAAAACTGATCGACCGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGCTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGga                                                                                                               <  1:207656/141‑1 (MQ=255)
                             cAAAAACTGATCGACCGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCGTGATGTGAAAGTTGCGAGAGTTATGGGTATGTTTGGCATTTCTAAGgaa                                                                                                              >  1:142190/1‑141 (MQ=255)
                             cAAAAACTGATCGACCGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGgaa                                                                                                              >  2:287898/1‑141 (MQ=255)
                                   cTGATCGACCGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTGGCGACAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGca                                                                                                        >  2:245786/1‑141 (MQ=255)
                                     gATCGACCGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGACGcaca                                                                                                      <  2:3428/141‑3 (MQ=255)
                                           ccGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACg                                                                                                <  1:287898/141‑1 (MQ=255)
                                                  gTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGttatta                                                                                         >  2:338359/1‑141 (MQ=255)
                                                     cGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTTCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAAc                                                                                      <  1:306187/141‑1 (MQ=255)
                                                     cGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAAc                                                                                      <  2:169097/141‑1 (MQ=255)
                                                           attCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGAGGTGAAAGTTGCGACAGTAATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAGGACGGTTATTAAACAATggg                                                                                >  2:7613/1‑140 (MQ=255)
                                                             tCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGa                                                                              <  1:241254/141‑1 (MQ=255)
                                                             tCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATATGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTATAGGGAAGAAGCAACAAGACGGGTATTAAACAATGGTgc                                                                              >  2:294849/1‑140 (MQ=255)
                                                                aGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGACAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACAt                                                                           <  2:219312/141‑1 (MQ=255)
                                                                   aaTATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGt                                                                        <  1:218810/141‑1 (MQ=255)
                                                                     tatGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTa                                                                      >  2:18618/1‑141 (MQ=255)
                                                                      atGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGACAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTaa                                                                     <  2:183969/141‑1 (MQ=255)
                                                                       cgtgaaaTCACATATGATGAAGCAATGGCGTGATATCAGGTATTTGAGCATGATTTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTaaa                                                                    <  2:29352/135‑1 (MQ=255)
                                                                         tgatagcacaTATGATGAAGCAATGGCGTTATATCACGTATCAGAGCATGGTGTAAAAGGAGCGAGAGTTAGGGGTACGTGTGGCATTTCTGAAGAAGAAGCAACCAGACGGTGATTAAACAATGGTGACATGTGTAAACg                                                                  >  2:130678/7‑141 (MQ=255)
                                                                           cTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGACAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAg                                                                >  2:82724/1‑141 (MQ=255)
                                                                                  atatGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCag                                                         >  1:172839/1‑141 (MQ=255)
                                                                                  atatGATGAAGCAAGGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGGTATGGGGATGTGTGGCCTTGCTAAGGAAGAAGCAACAAGACGGTTAATAAACAATGGTGACGTTGTTAAACGAGCAATGag                                                         >  2:250288/1‑141 (MQ=255)
                                                                                    atgatgAAGCAATGGCGTTATTTCAGGTATCTGAGCATGATGTGAAAGTTGCGACAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCagag                                                       <  2:49278/141‑1 (MQ=255)
                                                                                     tgatgaAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGACAGTTATGGGTCTGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTCTTAAACAACGGTGACATTGTTAAACGAGCAATCAgaga                                                      >  1:314330/1‑141 (MQ=255)
                                                                                     tgatgaAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGACAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAACCGCGCAAACAgaga                                                      >  2:205802/1‑141 (MQ=255)
                                                                                     tgatgaAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGACAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATCGTTAAACGAGCAATCAgaga                                                      <  1:209536/141‑1 (MQ=255)
                                                                                               aTGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGACAACCt                                            >  1:38285/1‑141 (MQ=255)
                                                                                                  gCGTAATATCAGGTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGACAACCTTag                                         <  1:213215/141‑1 (MQ=255)
                                                                                                              gTATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGACAACCTTAGGAGGGATTTaaa                             >  1:16780/1‑141 (MQ=255)
                                                                                                               tATCTGAGCATGATGTGAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTATACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGACAACCTTAGGAGGGATTTAAAt                            <  2:57385/141‑1 (MQ=255)
                                                                                                                   tGAGCATGATGTGAAAGTTGCGAGAGTTTTGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGACAACCTTAGGAGGGATTTAAATGAcc                        >  1:184386/1‑141 (MQ=255)
                                                                                                                    gAGCATGATGTGAAAGTTGCGACAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGACAACCTTAGGAGGGATTTAAATGACCa                       <  1:218795/141‑1 (MQ=255)
                                                                                                                       cATGATGTGAACGTTGCGACAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGACAACCTTAGGAGGGATTTAAATGACCAAAg                    >  1:342605/1‑141 (MQ=255)
                                                                                                                            tgtgAAAGTTGCGACAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGAAACCCTAAGAAGGGATTTAAATGAcagagttacaa               >  1:77690/1‑131 (MQ=255)
                                                                                                                             gtgAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGTATATAGCTATAGACAACCTTAGGAGGGATTTGAATGACCAAAGaacaac              >  1:284452/1‑141 (MQ=255)
                                                                                                                             gtgAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGACAACCTTAGGAGGGCTTTAAATGACCAAAGaacaac              >  1:300645/1‑141 (MQ=255)
                                                                                                                              tgAAAGTTGCGAGAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGACAACCTTAGGAGGGATTTAAATGACCAAAGaacaaca             <  1:227100/141‑1 (MQ=255)
                                                                                                                               aaaaGTTGGCATACTTATCGGTATGGTTTGCATTTTCAAGCAAAAAACAACAAGACGGTTATTAAACAATTGGGACATTGGTAAACGAGCAATCAGACATAGACAACCTCAGGAGGGATTTAAATTACCACAGaacaacaa            <  2:69478/140‑1 (MQ=255)
                                                                                                                                    ttGCGACAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGACAACCTTAGGAGGGATTTAAATGACCAAAGAACAACAACTTGc       <  2:327239/141‑1 (MQ=255)
                                                                                                                                         aCAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGACAACCTTAGGAGGGATTTAAATGACCAAAGAACAACAACTTGCAGAAc  <  1:282914/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                           
ACCTCATGATTGATGTTAAAGCAACCAATCAAAAACTGATCGACCGTTCAGTGCGTATTATTCAAGAAATATGTGCTATCACATATGATGAAGCAATGGCGTTATATCAGGTATCTGAGCATGATGTGAAAGTTGCGACAGTTATGGGTATGTGTGGCATTTCTAAGGAAGAAGCAACAAGACGGTTATTAAACAATGGTGACATTGTTAAACGAGCAATCAGAGATAGACAACCTTAGGAGGGATTTAAATGACCAAAGAACAACAACTTGCAGAAC  >  CP000730/225572‑225849

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A