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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,246,200 C→T 36.7% K100K (AAG→AAA)  znuA ← zinc transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,246,2000CT36.7% 47.7 / 44.5 76K100K (AAG→AAA) znuAzinc transporter subunit
Reads supporting (aligned to +/- strand):  ref base C (34/14);  new base T (10/18);  total (44/32)
Fisher's exact test for biased strand distribution p-value = 3.89e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.35e-01

CATCATCGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAACCCAAACG  >  minE/1246133‑1246266
                                                                   |                                                                  
catcatcGCCGTGATTACTTTTCATCAGTAGCGGTTTCTCATCTTCAAGCTGCGCAATCGTTAGCTGc                                                                    <  1:2337172/68‑1 (MQ=255)
catcatcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGc                                                                    <  1:1035706/68‑1 (MQ=255)
catcatcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGc                                                                    <  1:246693/68‑1 (MQ=255)
catcatcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGc                                                                    <  1:2975939/68‑1 (MQ=255)
catcatcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGc                                                                    <  1:430249/68‑1 (MQ=255)
catcatcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGc                                                                    <  1:1650111/68‑1 (MQ=255)
catcatcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGc                                                                    <  1:3430568/68‑1 (MQ=255)
catcatcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGc                                                                    <  1:1976900/68‑1 (MQ=255)
catcatcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGc                                                                    <  1:763417/68‑1 (MQ=255)
catcatcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGc                                                                    <  1:790253/68‑1 (MQ=255)
catcatcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGc                                                                    <  1:2582319/68‑1 (MQ=255)
catcatcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGc                                                                    <  1:1188568/68‑1 (MQ=255)
catcatcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGc                                                                    <  1:3259808/68‑1 (MQ=255)
catcatcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAACTGCGCAATCGTTACCTGc                                                                    <  1:691833/68‑1 (MQ=255)
    atcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGc                                                               >  1:3372543/1‑69 (MQ=255)
    atcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGc                                                               >  1:740424/1‑69 (MQ=255)
    atcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGc                                                               >  1:797587/1‑69 (MQ=255)
    atcGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGc                                                               >  1:644113/1‑69 (MQ=255)
           tGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGc                                                                    <  1:2837524/57‑1 (MQ=255)
                 cTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTg                                                  <  1:3003078/69‑1 (MQ=255)
                 cTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTg                                                  <  1:2408028/69‑1 (MQ=255)
                 cTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTg                                                  <  1:3127984/69‑1 (MQ=255)
                 cTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTg                                                  <  1:3042079/69‑1 (MQ=255)
                 cTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTg                                                  <  1:1464519/69‑1 (MQ=255)
                 cTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTg                                                  <  1:2541395/69‑1 (MQ=255)
                 cTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTg                                                  <  1:2832880/69‑1 (MQ=255)
                 cTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTg                                                  <  1:1317424/69‑1 (MQ=255)
                 cTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTg                                                  <  1:836770/69‑1 (MQ=255)
                 cTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTg                                                  <  1:2695147/69‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:2411837/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:290762/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:2500730/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:2348263/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:278424/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:2632738/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:2230644/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:2205374/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:1774293/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:467229/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:1702645/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:1626820/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:145883/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:1439400/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:1427476/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:1240309/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:1211979/54‑1 (MQ=255)
                  ttttCATCAGCAGCGGTTTCACATTCTCTAGCTGCGCAATCGTTACCTGTTTCg                                                                <  1:963904/54‑1 (MQ=255)
                                    tCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTg                                                  <  1:349273/50‑1 (MQ=255)
                                     cacaTCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTAcc                                            >  1:499367/1‑55 (MQ=255)
                                     cacaTCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATaaa                              >  1:3401986/1‑69 (MQ=255)
                                     cacaTCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATaaa                              >  1:1050775/1‑69 (MQ=255)
                                     cacaTCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATaaa                              >  1:1664103/1‑69 (MQ=255)
                                     cacaTCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATaaa                              >  1:2491832/1‑69 (MQ=255)
                                     caaaTCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATaaa                              >  1:1757556/4‑69 (MQ=255)
                                         tCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCt                          >  1:1411690/1‑69 (MQ=255)
                                            tctaGCTGCGCAATCGTTACCTGTTTCGCTTCAGGTAATTTACTTACCGGTTTTTGCATGAACGCTTcc                       >  1:3116904/4‑69 (MQ=255)
                                            tctaGCTGCGCAATCGTTACCTGTTTCGCTTCAGGTAATTTACTTACCGGTTTTTGCATGAACGCTTcc                       >  1:46330/4‑69 (MQ=255)
                                            tctaGCTGCGCAATCGTTACCTGTTTCGCTTCAGGTAATTTACTTACCGGTTTTTGCATGAACGCTTcc                       >  1:1533644/4‑69 (MQ=255)
                                            tctaGCTGCGCAATCGTTACCTGTTTCGCTTCAGGTAATTTACTTACCGGTTTTTGCATGAACGCTTcc                       >  1:186428/4‑69 (MQ=255)
                                            tctaGCTGCGCAATCGTTACCTGTTTCGCTTCAGGTAATTTACTTACCGGTTTTTGCATGAACGCTTcc                       >  1:722030/4‑69 (MQ=255)
                                            tctaGCTGCGCAATCGTTACCTGTTTCGCTTCAGGTAATTTACTTACCGGTTTTTGCATGAACGCTTcc                       >  1:2075065/4‑69 (MQ=255)
                                            tctaGCTGCGCAATCGTTACCTGTTTCGCTTCAGGTAATTTACTTACCGGTTTTTGCATGAACGCTTcc                       >  1:2327437/4‑69 (MQ=255)
                                            tctaGCTGCGCAATCGTTACCTGTTTCGCTTCAGGTAATTTACTTACCGGTTTTTGCATGAACGCTTcc                       >  1:786937/4‑69 (MQ=255)
                                            tctaGCTGCGCAATCGTTACCTGTTTCGCTTCAGGTAATTTACTTACCGGTTTTTGCATGAACGCTTcc                       >  1:1742494/4‑69 (MQ=255)
                                            tctaGCTGCGCAATCGTTACCTGTTTCGCTTCAGGTAATTTACTTACCGGTTTTTGCATGAACGCTTc                        >  1:1833162/4‑68 (MQ=255)
                                               aGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTc                        <  1:1313064/65‑1 (MQ=255)
                                               aGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTc                        <  1:2735605/65‑1 (MQ=255)
                                               aGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTc                        <  1:624776/65‑1 (MQ=255)
                                                 cTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGc                                   >  1:1454150/1‑52 (MQ=255)
                                                 cTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCAtctc                  >  1:2322415/1‑69 (MQ=255)
                                                 cTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCAtctc                  >  1:2469501/1‑69 (MQ=255)
                                                 cTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCAtctc                  >  1:419975/1‑69 (MQ=255)
                                                 atGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATaaa                              >  1:2578491/2‑57 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCa           >  1:639494/1‑66 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAAc         >  1:701803/1‑68 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAAc         >  1:1220690/1‑68 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAAc         >  1:1163797/1‑68 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAAc         >  1:870210/1‑68 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAAc         >  1:1098311/1‑68 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAAc         >  1:593766/1‑68 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAAc         >  1:1788797/1‑68 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAAc         >  1:350911/1‑68 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAAc         >  1:197151/1‑68 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAAc         >  1:3272829/1‑68 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAAc         >  1:2283501/1‑68 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAAc         >  1:254367/1‑68 (MQ=255)
                                                           gTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAAc         >  1:2573078/1‑68 (MQ=255)
                                                              aCCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAACCCaa     >  1:2628198/1‑69 (MQ=255)
                                                                 tGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAACCCAAACg  >  1:3022315/1‑69 (MQ=255)
                                                                 tGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAACCCAAACg  >  1:2332025/1‑69 (MQ=255)
                                                                  gCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAACCCAAACg  >  1:2692221/1‑68 (MQ=255)
                                                                   |                                                                  
CATCATCGCCGTGAATACTTTTCATCAGTAGCGGTTTCACATCTTCAAGCTGCGCAATCGTTACCTGCTTCGCTCCTGGTAATTTGCTTACCGGTTTTTGCATAAACGCTTCCATCTCCGGGCCAACCCAAACG  >  minE/1246133‑1246266

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A